#! /bin/bash

#+
# NAME:
#	sync_ips_daily
# PURPOSE:
#	Controls the processing of new IPS data arriving from Nagoya.
# CALLING SEQUENCE:
#	as cron job:
#	bash --login -c "sync_ips_daily"
#
#	interactive:
#	sync_ips_daily [--with-correlations]
#		- gets new data from Nagoya site
#		- if no new data available
#			- only update all images
#			  on the website (correlation graphs will only
#			  be updated if --with-correlations is set)
#		- if new data are available
#			- run corotating tomography
#			- run time-depenent tomography
#			- update images on website (incl. correlations)
#			- update moview on website
#
#	Several of the components can be run individually:
#
#	sync_ips_daily --download-only
#		checks Nagoya site for new IPS data and downloads
#		if new IPS data are available
#
#	sync_ips_daily --tomography
#		runs the tomography (both corotating and time-dependent,
#		and updates the all images (incl. correlations) and
#		movies on the IPS website
#
#	sync_ips_daily --image-update [--with-correlations]
#		updates all images on the website. The correlations graphs
#		are updated only if --with-correlations is set too
#
#	sync_ips_daily --movie-update
#		updates all movies on the website.
#		
# INPUTS:
# OPTIONAL INPUT PARAMETERS:
#	--tomography	if set the script jumps straight to running
#			the tomography programs, bypassing the download
#			of new daily IPS files.
#	--download-only	if set the script just runs the download script
#			and does not run the tomography programs
#
#	--image-update	only updates images on IPS website
#			(incl. correlation graphs if --with-correlations
#			is set.
#	--with-correlations
#			updates correlation graphs, if set in conjunction
#			with --image-updates
#
#	--movie-update	only updates movies on IPS website
#
#	--dry-run	a 'dry-run' currently will run the tomography
#			in $TUB, and suppress copying of images and html
#			files to the IPS website.
#
#	We have available both NSO/NOAA and WSO/NOAA magnetic field data.
#	These are added to the processing by defining the env vars BB_PREFIXES,
#	BB_PREFIXES_SLOW and BB_PREFIXES_FAST.
#	To use the same magnetic data for both corotating and time-dependent
#	tomography used BB_PREFIXES:
#		BB_PREFIXES='wson'		only WSO/NOAA data
#		BB_PREFIXES='nson'		only NSO/NOAA data
#		BB_PREFIXES='wson nson'		both WSO/NOAA and NSO/NOAA
#	To use different magnetic fields for corotating and time-dependent
#	tomography set the pair BB_PREFIXES_SLOW and BB_PREFIXES_FAST to the
#	desired magnetic data.
# CALLS:
#	sync_ips_mirror, ipsd, ipsdt, vox_update
#	run_mean, run_marker
# PROCEDURE:
#	Finally one or more tomography programs are called to update the
#	latest tomographic reconstructions.
#
#	People on the honcho list receive several email notifications
#	when a part of the script completes.
#	Multiple email addresses need to be separated by a space.
#
#	The IDL display software differentiates between corotating
#	and time-dependent tomography output files by checking the 
#	'marker' value. This value is coded in the filename, and is present
#	in the header under the key 'Rotation counter'.
#
#	For a corotating file the marker value in the header MUST be zero;
#	and the marker is NOT encoded in the filename.
#
#	For a time-dependent file the marker value identifies all files
#	associated with the same tomography run. It has a value of 1 or higher.
#	The marker is coded in the filename as a 5-digit integer.
# MODIFICATION HISTORY:
#	JAN-2001, Paul Hick (UCSD/CASS)
#	SEP-2001, Paul Hick (UCSD/CASS)
#		Added honcho email list
#	AUG-2002, Paul Hick (UCSD/CASS)
#		Removed explicit calls to bash startup scripts
#		/etc/profile and ~/.bash_profile.
#	OCT-2002, Paul Hick (UCSD/CASS)
#		Rewrite of download section. Now uses Perl script 'mirror'
#		Also added the -tomography keyword.
#	OCT-2002, Paul Hick (UCSD/CASS)
#		The script does not abort anymore when the corotating tomography
#		fails, but continues with the time-dependent program.
#		All image updates are now done after both tomography programs
#		have been run. The intermediate update of the corotating images
#		prior to running the time-dependent tomography has been dropped.
#	JUN-2003, Paul Hick (UCSD/CASS)
#		Added calls to gzip to compress all nv3d*, etc., both raw
#		and final versions.
#	JUL-2003, Paul Hick (UCSD/CASS)
#		Removed call to 'idl run_map'
#	NOV-2003, Paul Hick (UCSD/CASS)
#		Removed compression of final files in this script using a single
#		gzip -f after the call to run_marker or run_mean. Instead this is now
#		done by the IDL procedure vu_write on a file by file basis.
#		The gzip -f call caused problems for the hourly forecast run while
#		run_marker was creating new final files. For some time the old
#		(gzipped) final files would coexist with the new (unzipped) final
#		files (until gzip -f was completed). An hourly forecast run during
#		this time would find multiple files referring to the same time.
#		The results are blank maps at the hourly forecast time.
#	AUG-2004, Paul Hick (UCSD/CASS)
#		Modified selection of magnetic field data by env variables.
#	APR-2011, John Clover (UCSD/CASS)
#		Modified to use ipstd20n_intel and output/process nv3h files.
#	APR-2013, Paul Hick (UCSD/CASS; pphick@ucsd.edu)
#		Substantial cleanup. More documentation.
#		Switched to long options.
#-

. tiny_bits.sh
__CALLER__=`basename $0`
__TIME_TAG__="%m/%d %H:%M"

image_update () {		# Update of all images and html files for IPS website

	local __CALLER__="image_update"

	# The egrep command makes spurious IDL messages go away

	if [ $WITH_CORRELATIONS -eq 0 ]; then
		export NOCORRELATION=1
	fi

	idl -quiet run_map.pro 2>&1 | egrep -v " Compiled module:| Loaded DLM:| Program caused arithmetic error:"

	unset NOCORRELATION
}

movie_update () {		# Update all the movies on the IPS website

	local __CALLER__="movie_update"

	# The egrep command makes spurious IDL messages go away

	idl -quiet run_movie.pro 2>&1 | egrep -v " Compiled module:| Loaded DLM:| Program caused arithmetic error:"

	# Remove all mng movies

	$RM -f $HTM/forecast/slow/current/*movie.mng
	$RM -f $HTM/forecast/fast/current/*movie.mng

	# === Create vox files ==============
	# DISABLED, PPH 2013-04

	#if [ "$(date +%d)" == "1" ]; then
	#	tiny_say "update vox files (slow)"
	#	vox_update.py -source=$slow_final -destination=$slow_vox -nv_prefix=nv3d
	#	# Final files are not produced anymore
	#	tiny_say "update vox files (fast)"
	#	vox_update.py -source=$fast_final -destination=$fast_vox -nv_prefix=nv3h
	#fi
}

align_nv_and_nson () {

	local __CALLER__="align_nv_and_nson"

	# If there are no nson files at all, then assume that
	# magnetic fields were not produced at all, so skip
	# the alignment.

	if [ `ls $PWD/nson* 2> /dev/null | egrep -v \.gz$ | wc -l` -eq 0 ]; then
		tiny_say "no uncompressed (new) nson files present"
		return 0
	fi

	# Move unmatched nv3d files to subdirectory $slow_raw/ice
	# Delete unmatched nson files.

	local prefix
	local kind=$1
	if [ $kind = "slow" ]; then
		prefix="nv3d"
	else
		prefix="nv3h"
	fi

	tiny_say "align $prefix and nson files in $PWD"

	local f
	local g

	ls $PWD/nson* 2> /dev/null | egrep -v \.gz$ |
	while read f; do				# Loop over uncompressed (new) nson files
		#if [[ ! $f =~ \.gz ]]; then	# Only check uncompressed (new) files
			g=`basename $f`
			g="$PWD/${g/nson/$prefix}"
			if [ ! -f $g ]; then	# No matching nv3d file
				$RM $f				# Remove nson file
			fi
		#fi
	done

	ls $PWD/$prefix* 2> /dev/null | egrep -v \.gz$ |
	while read f; do				# Loop over nv3d files
		#if [[ ! $f =~ \.gz ]]; then	# Skip gzipped files
			g=`basename $f`
			g="$PWD/${g/$prefix/nson}"
			if [ ! -f $g ]; then	# No matching nson file
				tiny_warn "WARNING: removed $f: no matching nson file !!!"
				$RM $f				# Remove nv3d file
			fi
		#fi
	done

	return 0
}

compress_raw_files () {
	local __CALLER__="compress_raw_files"

	# Compress all new raw files

	for f in $PWD/*.*; do
		if [[ ! $f =~ \.gz$ ]]; then 
			$GZIP $f
		fi
	done
}

fix_slow_raw_files () {

	# The new version of the corotating tomography creates
	# files in time-dependent format:
	# - the filename contains a 'marker' value of 1
	# - the 'Rotation counter' in the header will be 1
	# To make sure the IDL software treats these file as
	# corotating files the marker needs to be removed from the
	# the filename and the rotation counter needs to be set to zero.

	# THIS REALLY NEEDS TO BE FIXED IN THE TOMOGRAPHY PROGRAM ITSELF.
	local __CALLER__="remove_marker_from_filename"

	# The regex will skip gzipped files. Only uncompressed files,
	# presumably just created by the tomography, are processed.
	# The sed command will rewrite each file, setting the marker value
	# in the header to zero.
	# The mv command will rename the file, removing the marker.

	for f in `ls $PWD/*.*_*`; do
		if [[ $f =~ (.+)_[0-9]{5}$ ]]; then
			sed --in-place 's/; Rotation counter: 1/; Rotation counter: 0/' $f
			$MV $f ${BASH_REMATCH[1]}
		fi
	done

}

source_surface_update () {
	local __CALLER__="source_surface"
	mag_noaa.py --ftp --sync --obs=nso_ktpk 2>&1 | egrep -v " Compiled module:| Loaded DLM:| Program caused arithmetic error:| READFITS: EOF"
}

declare -A VALID_OPTIONS
declare -A VALID_DESCRIPTION
VALID_OPTIONS=( \
	[-t,--tomography-only]=bool-TOMOGRAPHY_ONLY			\
	[-d,--download-only]=bool-DOWNLOAD_ONLY				\
	[-s,--source-surface-only]=bool-SOURCE_SURFACE_ONLY	\
	[-i,--image-update]=bool-IMAGE_UPDATE				\
	[-c,--with-correlations]=bool-WITH_CORRELATIONS		\
	[-m,--movie-update]=bool-MOVIE_UPDATE				\
	[--honcho]=HONCHO									\
)
VALID_DESCRIPTION=( \
	[-t,--tomography-only]="skip IPS download, and only run tomography"					\
	[-d,--download-only]="only download IPS data, do not run tomography"				\
	[-s,--source-surface-only]="only create magnetic source surface maps"				\
	[-i,--image-update]="updates images on IPS website"									\
	[-c,--with-correlations]="creates correlation images if used with --image-update"	\
	[-m,--movie-update]="updates movies on IPS website"									\
	[--honcho]="email address to receive completion notifications by email"				\
)
. get_options.sh
get_options $*
unset get_options

((SILENT=2-$VERBOSE))
export SILENT		# For IDL programs
export DRYRUN

CP="cp"
MV="mv"
RM="rm"
GZIP="gzip -f"
if [ $VERBOSE -ge 2 ]; then
	CP+=" -v"
	MV+=" -v"
	RM+=" -v"
	GZIP+=" -v"
fi

# --image-update set: update images, and exit

if [ $IMAGE_UPDATE -eq 1 ]; then
	image_update				# Create images for website
	exit 0
fi

# --movie-update set: update movies, and exit

if [ $MOVIE_UPDATE -eq 1 ]; then
	movie_update
	exit 0
fi

if [ $SOURCE_SURFACE_ONLY -eq 1 ]; then
	source_surface_update
	exit 0
fi

if [ $TOMOGRAPHY_ONLY -eq 0 ]; then

	# Check Nagoya website for new data.

	sync_ips_realtime $verbose $debug $dryrun $HONCHO
	exit_code=$?

	if [ $exit_code -eq 1 ]; then		# Error in sync_ips_real_time
		tiny_die "tomography not run"
	fi

	if [ $DOWNLOAD_ONLY -eq 1 ]; then	# Only download requested
		exit 0
	fi

	# Suppress output from hourly image updates

	((SILENT+=1))
	export SILENT

	image_update						# Create images for website

	((SILENT-=1))
	export SILENT

	if [ $exit_code -eq 2 ]; then		# No new data; don't run tomography
		exit 0
	fi

fi

# Run tomography using new IPS data

start_time=$(date)

# Set type of magnetic data.
# The tomography needs source surface magnetic field data to calculate
# the heliospheric magnetic field.
# These files are created by XuePu hcss program from photospheric maps
# downloaded from some remote site.
# This process is controlled by cronjobs running the Python script
# mag_noaa.py (which in turn calls XuePu's program from the IDL
# wrapper xhcs.pro).

# mag_wso_noaa="wso_noaa=wso_noaa[4]_[3]_[1].fts,$DAT,map,wso_noaa,hcss"
mag_nso_noaa="nso_noaa=nso_ktpk[4]_[3].fts,$DAT,map,nso_ktpk,hcss"

if [[ "$BB_PREFIXES $BB_PREFIXES_SLOW" =~ wson ]]; then
	mag_slow="$mag_slow $mag_wso_noaa"
fi

if [[ "$BB_PREFIXES $BB_PREFIXES_SLOW" =~ nson ]]; then
	mag_slow="$mag_slow $mag_nso_noaa"
fi

if [[ "$BB_PREFIXES $BB_PREFIXES_FAST" =~ wson ]]; then
	mag_fast="$mag_fast $mag_wso_noaa"
fi

if [[ "$BB_PREFIXES $BB_PREFIXES_FAST" =~ nson ]]; then
	mag_fast="$mag_fast $mag_nso_noaa"
fi

# === Initialization section =================


# Input for the tomography programs.
# These files contain all the input parameters requested by the tomography
# programs. They are fed to the program by piping them to standard input.

#nagoya_slow=$SYS/nagoya/nagoya_forecast.slow-gonly
nagoya_slow=$SYS/nagoya/nagoya_forecast.slow_10n_inp_mag

#nagoya_fast=$SYS/nagoya/nagoya_forecast.fast_20n
#nagoya_fast=$SYS/nagoya/nagoya_forecast.fast_20n_inp
nagoya_fast=$SYS/nagoya/nagoya_forecast.fast_20n_inp_mag

# The tomography program write output to the working directory.
# These 'raw' files are written to directories slow/raw (for
# corotating tomography) and fast/raw (for time-dependent tomography).

# The raw files can be post-processed to create 'smoothed' final
# files. The post-processing is done by IDL programs (run_mean.pro for
# corotating tomography); run_marker.pro for time-dependent tomography).
# These final files are written to directories slow/final and fast/final.

# Currently only the final files for the corotating tomography are
# created. The time-dependent tomography files are not smoothed anymore,
# so the fast/final directory is not used anymore.

slow_raw=$NAGOYA/slow/raw
fast_raw=$NAGOYA/fast/raw
slow_final=$NAGOYA/slow/final
fast_final=$NAGOYA/fast/final
slow_vox=$NAGOYA/slow/vox
fast_vox=$NAGOYA/fast/vox

# Check for magnetic field updates

source_surface_update

# ===  Run corotating tomography program =========

# The program takes its input from  the file $nagoya_slow.
# This starts the program in forecast mode. The modified Julian
# reference time is left blank  so the default calculated by
# the tomography program is accepted.

# The tomography program writes its output into the working
# directory, so we cd to the directory where we want the output.
# If an error occurs a message is output, but the script does not abort.

savepwd=$PWD

if [ $DRYRUN -eq 0 ]; then
	if [ -d $slow_raw/transit ]; then
		rm -rf $slow_raw/transit
	fi
	mkdir $slow_raw/transit
	cd $slow_raw/transit
else
	cd $TUB
fi

tiny_yell "run co-rotating tomography in $PWD"
tiny_yell "magnetic field used is '$mag_slow'"

#ipsd $mag_slow < $nagoya_slow > $TUB/cron_ipsd.txt
# When the magnetic field works at higher resolutions this can _10n (BVJ)

# NOTE: the wildcard (*) after the celias filename is necessary!!
# Without the wildcard the celias file name is not picked up by the tomography
# program even though the file exists. If that bug gets fixed some day the
# wildcard may need to be removed.

ipstd_20n_inp_mag_intel ace=acesw_[4].hravg,$DAT/insitu/ celias=$DAT/insitu/realcelias/celias_realtime.hravg* $mag_slow < $nagoya_slow > $TUB/cron_ipsd.txt
case $? in
1) status=finished ;;
*) status=error ;; 
esac

tiny_yell "corotating tomography $status"
if [ -n "$HONCHO" ]; then
	date | mail -s "Corotating tomography $status" $HONCHO
fi

if [ $status = "finished" ]; then

	# Clean up the output from the tomography run in $slow_raw/transit

	if [ -n "$mag_slow" ]; then	# in $PWD: sync plasma and magnetic files
		align_nv_and_nson slow
	fi
	fix_slow_raw_files			# in $PWD: remove markers; fix headers
	compress_raw_files			# in $PWD: compress files

	if [ $DRYRUN -eq 0 ]; then
		$MV $PWD/*.* $slow_raw	# Move the clean output to $slow_raw
		cd $slow_raw
		rmdir $slow_raw/transit	# Remove the transit directory
	fi

	# Produce the final smoothed files in directory $slow_final

	tiny_yell "creating final corotating tomography files (run_mean)"
	idl -quiet run_mean.pro 2>&1 | egrep -v " Compiled module:| Loaded DLM:| Program caused arithmetic error:"

	# Archive raw files (in $slow_raw) and final files (in $slow_final)
	# that are older than about one Carrington rotation into
	# subdirectories $slow_raw/ice and $slow_final/ice, respectively.

	idl -quiet -e "forecast_ice,'slow',silent=$SILENT" 2>&1 | egrep -v " Compiled module:| Loaded DLM:| Program caused arithmetic error:"
fi

# ===  Run time-dependent tomography program ===========

# The tomography program writes its output into the working
# directory, so we cd to the directory where we want the output.
# If an error occurs a message is output, but the script does not abort.

# Currently (2013-04) the nv3h files are created at 10 degree resolution,
# while the nson files are created at 20 degree resolution.

if [ $DRYRUN -eq 0 ]; then
	cd $fast_raw
else
	cd $TUB
fi

tiny_yell "run time-dependent tomography in $PWD"
tiny_yell "magnetic field used is '$mag_fast'"

# NOTE: the wildcard (*) after the celias filename is necessary!!
# Without the wildcard the celias file name is not picked up by the tomography
# program even though the file exists. If that bug gets fixed some day the
# wildcard may need to be removed.

ipstd_20n_inp_mag_intel ace=acesw_[4].hravg,$DAT/insitu/ celias=$DAT/insitu/realcelias/celias_realtime.hravg* $mag_fast < $nagoya_fast > $TUB/cron_ipsdt.txt
case $? in
1) status=finished ;;
*) status=error ;;
esac

tiny_yell "time-dependent tomography $status"
if [ -n "$HONCHO" ]; then
	date | mail -s "Time-dependent tomography $status" $HONCHO
fi

##
# removed by John Clover 08/29/2011 -- final files not used
#
# move negoya file, if it exists
#mv negoya.2011 $NAGOYA/rtsources/nagoya.2011
#cp $DAT/nagoya/rtsources/nagoya.2011 $DAT/nagoya/rtsources/nagoya.2012
# at the beginning of the year 2013 put in place the following lines:
#mv negoya.2012 $NAGOYA/rtsources/nagoya.2013
# for now negoya is 2012 only but if the tomo. program begins to output 2013
# the last mv below should override the previous command

# WHAT IS THIS FOR? PPH 2013-04

$MV nggoya.2013 $NAGOYA/rtsources/nagoya.2013
$MV negoya.2013 $NAGOYA/rtsources/nagoya.2013

if [ $status = finished ]; then

	if [ -n "$mag_fast" ]; then	# in $PWD: sync new plasma and magnetic files
		align_nv_and_nson fast
	fi
	compress_raw_files			# in $PWD: gzip files

 	#tiny_say "creating final time-dependent tomography files (run_marker)"
	#export NV_PREFIX="nv3h"
	#idl -quiet run_marker.pro
	#unset NV_PREFIX

	# Archive raw files (in $fast_raw) and final files (in $fast_final)
	# that are older than about one Carrington rotation into
	# subdirectories $fast_raw/ice and $fast_final/ice, respectively.

	idl -quiet -e "forecast_ice,'fast',silent=$SILENT" 2>&1 | egrep -v " Compiled module:| Loaded DLM:| Program caused arithmetic error:"

fi

cd $savepwd

# === Create images and animations (daily) =============

WITH_CORRELATIONS=1

tiny_yell "update images for website"
image_update		# Create images for website

tiny_yell "update movies for website"
movie_update		# Create movies for website

if [ -n "$HONCHO" ]; then
	echo "Start at $start_time; Finished at $(date)" | mail -s"Nagoya IPS tomography finished" $HONCHO
fi

tiny_done "done"