metis_l1_prep.pro

pro metis_l1_prep

	; start the log

	journal, 'output/metis_l1_prep_log.txt'

	; some definitions

	metis_datatype = list( $
		'VL image', $						; 0
		'UV image', $						; 1
		'PCU accumulation matrix', $		; 2
		'VL temporal standard deviation', $	; 3
		'UV temporal standard deviation', $	; 4
		'VL cosmic-ray matrix', $			; 5
		'UV cosmic-ray matrix', $			; 6
		'PCU event list', $					; 7
		'PCU test event list', $			; 8
		'VL light-curve' $					; 9
	)

	metis_obj_size = list( $
		2048L, $					; 0
		1024L, $					; 1
		1024L, $					; 2
		2048L, $					; 3
		1024L, $					; 4
		2048L, $					; 5
		1024L $						; 6
	)

	; read the auxiliary input file

	input = json_parse('input/contents.json', /toarray, /tostruct)

	journal, 'File ' + input.file_name

	; load the spice kernels

	kernels = [ $
		input.tls_file_name, $
		input.tsc_file_name $
	]

	; load the spice kernels

	cspice_furnsh, kernels

	journal, 'SPICE kernel files correctly loaded:'
	journal, '  sclk kernel = ' + input.tsc_file_name
	journal, '  leap seconds kernel = ' + input.tls_file_name

	; read l0 fits structure

	fits_info, input.file_name, n_ext = n_ext, extname = extname, /silent

	; read the primary hdu

	ext_no = 0
	data = mrdfits(input.file_name, ext_no, primary_header, /silent)

	; if the data is not an image, read the data binary-table extension

	if fxpar(primary_header, 'NAXIS') eq 0 then begin
		ext_no += 1
		data_bin_table = mrdfits(input.file_name, ext_no, data_extension_header, /silent)
	endif else data_bin_table = !null

	; read the metadata extension

	ext_no += 1
	metadata_bin_table = mrdfits(input.file_name, ext_no, metadata_extension_header, /silent)

	; identify the data product and its nominal size

	datatype = fxpar(metadata_extension_header, 'DATATYPE')

	if datatype le 6 then begin
		naxis = 2
		naxis1 = metis_obj_size[datatype]
		naxis2 = naxis1
	endif else begin
		naxis = 0
	endelse

	; if the data product is an accumulation matrix, look for the accumulation vector extension and read it if it exists

	if datatype eq 2 then begin
		if fxpar(metadata_extension_header, 'M') eq 256 then begin
			ext_no += 1
			accumul_vector = mrdfits(input.file_name, ext_no, vector_extension_header, /silent)
		endif else accumul_vector = !null
	endif

	journal, 'L0 FITS file correctly read:'
	journal, '  datatype = ' + string(datatype, format = '(I0)')
	if datatype le 6 then journal, '  size = ' + string(naxis1, format = '(I0)') + '×' + string(naxis2, format = '(I0)')

	; NOTE - the radialization extension is ignored

	; read the planning data

	planning_data = json_parse(input.planning_file_name, /toarray, /tostruct)

	; definitions for the primary header
	; version of the fits file

	version = string(input.l1_version + 1, format = '(I02)')

	; creation and acquisition times in utc

	date = date_conv(systime(/julian, /utc), 'FITS')

	obt_beg = fxpar(primary_header, 'OBT_BEG')
	obt_end = fxpar(primary_header, 'OBT_END')
	obt_avg = (obt_beg + obt_end) / 2.0D

	date_beg = solo_obt2utc(decode_obt(obt_beg, /from_double))
	date_end = solo_obt2utc(decode_obt(obt_end, /from_double))
	date_avg = solo_obt2utc(decode_obt(obt_avg, /from_double))

	date_beg_string = strmid(date_beg, 0, 19)
	date_beg_string = date_beg_string.replace('-', '')
	date_beg_string = date_beg_string.replace(':', '')

	journal, 'UTC time of start acquisition = ' + date_beg

	; name of the fits file

	file_name_fields = strsplit(fxpar(primary_header, 'FILENAME'), '_', /extract)

	file_name = 'solo_L1_' + file_name_fields[2] + '_' + date_beg_string + '_V' + version + '.fits'
	out_file_name = 'output/' + file_name

	; instrument keywords

	if datatype eq 0 or datatype eq 3 or datatype eq 5 or datatype eq 9 then begin
		filter = 'VL'
		wavelnth = 610.0
		wavemin = 580.0
		wavemax = 640.0
		waveband = 'Visible light 580-640 nm'
	endif else begin
		filter = 'UV'
		wavelnth = 121.6
		wavemin = 111.6
		wavemax = 131.6
		waveband = 'H I Lyman-alpha 121.6 nm'
	endelse
	detector = filter + 'D'
	telescope = 'SOLO/Metis/' + detector

	; campaign keywords

	obs_id_fields = strsplit(planning_data.obs_id, '_', /extract)
	soop_type = obs_id_fields[2]
	obs_type = obs_id_fields[4]

	; build the fits file extensions

	; join the metadata extension header to the primary header removing unwanted keywords

	i = where(strmid(primary_header, 0, 8) eq 'COMP_RAT')
	j = where(strmid(metadata_extension_header, 0, 8) eq 'EXTNAME ')
	k = where(strmid(metadata_extension_header, 0, 8) eq 'TFORM1  ')

	primary_header = [ $
		primary_header[0 : i], $
		metadata_extension_header[j + 1 : k - 1], $
		primary_header[i + 1: *] $
	]

	; rebin the image if binning was applied during the acquisition

	if datatype le 6 then begin
		if fxpar(primary_header, 'COMPR') then $
			bin_type = fxpar(primary_header, 'B0_BIN') else bin_type = 0

		pol_id = fxpar(primary_header, 'POL_ID')
		fpfilt = fxpar(primary_header, 'VLFPFILT', count = count)
		if count gt 0 and pol_id eq 0 and fpfilt eq 0 and bin_type eq 0 then bin_type = 1

		bin_fact = 2. ^ bin_type
		if bin_fact gt 1. then begin
			data = rebin(data, naxis1 / bin_fact, naxis2 / bin_fact)
			data = data * bin_fact^2

			if ~ isa(comment) then comment = !null
			comment = [comment, 'Image was rebinned according to the commanded binning factor.']

			journal, 'Data was binned during acquisition:'
			journal, '  binning = ' + string(bin_fact, format = '(I1)') + '×' + string(bin_fact, format = '(I1)')
			journal, '  data was correctly rebinned:'
			journal, '    new size = ' + string(naxis1 / bin_fact, format = '(I0)') + '×' + string(naxis1 / bin_fact, format = '(I0)')
		endif else begin
			journal, 'Data was not binned during acquistion.'
		endelse
	endif

	; correct for the effective exposure time

	telapse = float(obt_end - obt_beg)

	dit = fxpar(metadata_extension_header, 'DIT')
	ndit = fxpar(metadata_extension_header, 'NDIT', missing = 1.)
	ndit1 = fxpar(metadata_extension_header, 'NDIT1', missing = 1.)
	ndit2 = fxpar(metadata_extension_header, 'NDIT2', missing = 1.)

	if datatype le 6 then begin
		xposure = dit/1000. * ndit * ndit1 * ndit2
		nsumexp = fix(ndit * ndit1 * ndit2)
		data = data * nsumexp

		if max(data, /nan) gt 32768 then data = long(data) else data = fix(data)

		datamin = min(data, /nan)
		datamax = max(data, /nan)

		fxaddpar, primary_header, 'DATAMIN', datamin
		fxaddpar, primary_header, 'DATAMAX', datamax

		if ~ isa(comment) then comment = !null
		comment = [comment, 'Image values were corrected for the total exposure time.']

		if nsumexp gt 1 then journal, 'Image values were corrected for the total exposure time.'
	endif else begin
		xposure = dit/1000.
		nsumexp = 1
		data = !null
	endelse

	; adjust the primary header (it is almost the same for all data product types)

	fxaddpar, primary_header, 'FILENAME', file_name
	fxaddpar, primary_header, 'PARENT', file_basename(input.file_name), 'Name of the parent file that got processed to the current one', before = 'APID'
	fxaddpar, primary_header, 'DATE', date, 'Date and time of FITS file creation', before = 'OBT_BEG'
	fxaddpar, primary_header, 'DATE-OBS', date_beg, 'Same as DATE-BEG', before = 'OBT_BEG'
	fxaddpar, primary_header, 'DATE-BEG', date_beg, 'Start time of observation', before = 'OBT_BEG'
	fxaddpar, primary_header, 'DATE-AVG', date_avg, 'Average time of observation', before = 'OBT_BEG'
	fxaddpar, primary_header, 'DATE-END', date_end, 'End time of observation', before = 'OBT_BEG'
	fxaddpar, primary_header, 'TIMESYS', 'UTC', 'System used for time keywords', before = 'OBT_BEG'
	fxaddpar, primary_header, 'TIMRDER', 0.0, '[s] Estimated random error in time values', before = 'OBT_BEG'
	fxaddpar, primary_header, 'TIMSYER', 0.0, '[s] Estimated systematic error in time values', before = 'OBT_BEG'
	fxaddpar, primary_header, 'LEVEL', 'L1'
	fxaddpar, primary_header, 'CREATOR', 'metis_l1_prep.pro'
	fxaddpar, primary_header, 'VERS_SW', input.sw_version
	fxaddpar, primary_header, 'OBSRVTRY', 'Solar Orbiter', 'Satellite name', before = 'INSTRUME'
	fxaddpar, primary_header, 'TELESCOP', telescope, 'Telescope that took the measurement', before = 'INSTRUME'
	fxaddpar, primary_header, 'DETECTOR', detector, 'Subunit/sensor', before = 'DATAMIN'
	fxaddpar, primary_header, 'OBJECT', 'TBD', 'The use of the keyword OBJECT is [TBD]', before = 'DATAMIN'
	fxaddpar, primary_header, 'OBS_MODE', planning_data.obs_mode, 'Observation mode', before = 'DATAMIN'
	fxaddpar, primary_header, 'OBS_TYPE', obs_type, 'Encoded version of OBS_MODE', before = 'DATAMIN'
	fxaddpar, primary_header, 'FILTER', filter, 'Filter used to acquire this image', before = 'DATAMIN'
	fxaddpar, primary_header, 'WAVELNTH', wavelnth, '[nm] Characteristic wavelength of observation', before = 'DATAMIN'
	fxaddpar, primary_header, 'WAVEMIN', wavemin, '[nm] Min. wavelength where response > 0.05 of max.', before = 'DATAMIN'
	fxaddpar, primary_header, 'WAVEMAX', wavemax, '[nm] Max. wavelength where response > 0.05 of max.', before = 'DATAMIN'
	fxaddpar, primary_header, 'WAVEBAND', waveband, 'Bandpass description', before = 'DATAMIN'
	fxaddpar, primary_header, 'XPOSURE', xposure, '[s] Total effective exposure time', before = 'DATAMIN'
	fxaddpar, primary_header, 'NSUMEXP', nsumexp, 'Number of detector readouts summed together', before = 'DATAMIN'
	fxaddpar, primary_header, 'TELAPSE', telapse, '[s] Elapsed time between beginning and end of observation', before = 'DATAMIN'
	fxaddpar, primary_header, 'SOOPNAME', planning_data.soop_name, 'Name of the SOOP campaign that the data belong to', before = 'DATAMIN'
	fxaddpar, primary_header, 'SOOPTYPE', soop_type, 'Campaign ID(s) that the data belong to', before = 'DATAMIN'
	fxaddpar, primary_header, 'OBS_ID', planning_data.obs_id, 'Unique ID of the individual observation', before = 'DATAMIN'
	fxaddpar, primary_header, 'TARGET', 'TBD', 'Type of target from planning', before = 'DATAMIN'
	fxaddpar, primary_header, 'BSCALE', 1, 'Ratio of physical to array value at 0 offset', before = 'DATAMIN'
	fxaddpar, primary_header, 'BZERO', 0, 'Physical value for the array value 0', before = 'DATAMIN'
	fxaddpar, primary_header, 'BTYPE', metis_datatype[datatype], 'Science data object type', before = 'DATAMIN'
	fxaddpar, primary_header, 'BUNIT', 'DN', 'Units of physical value, after application of BSCALE and BZERO', before = 'DATAMIN'
	fxaddpar, primary_header, 'IDB_VERS', input.idb_version, '', before = 'HDR_VERS'
	fxaddpar, primary_header, 'INFO_URL', 'http://metis.oato.inaf.it', 'Link to more information on the instrument data', before = 'HISTORY'

	if datatype le 6 then begin
		fxaddpar, primary_header, 'NBIN1', bin_fact, 'Binning factor in the dimension 1', before = 'COMPRESS'
		fxaddpar, primary_header, 'NBIN2', bin_fact, 'Binning factor in the dimension 2', before = 'COMPRESS'
		fxaddpar, primary_header, 'NBIN', bin_fact * bin_fact, 'Product of all NBIN values above', before = 'COMPRESS'
		fxaddpar, primary_header, 'PXBEG1', 1, 'First pixel that has been read out in dimension 1', before = 'COMPRESS'
		fxaddpar, primary_header, 'PXBEG2', 1, 'First pixel that has been read out in dimension 2', before = 'COMPRESS'
		fxaddpar, primary_header, 'PXEND1', naxis1, 'Last pixel that has been read out in dimension 1', before = 'COMPRESS'
		fxaddpar, primary_header, 'PXEND2', naxis2, 'Last pixel that has been read out in dimension 2', before = 'COMPRESS'
	endif

	; read the house-keeping telemetry

	hk_table = json_parse(input.hk_file_name, /toarray, /tostruct)

	; replace raw values with calibrated values in the primary header

	empty_params = !null

	if datatype eq 0 or datatype eq 3 or datatype eq 5 then begin

		; NOTE - DACPOL parameters are not calibrated since a calibration curve does not exist in the IDB. Their calibration in physical units (e.g., voltages or angles) should be done later

		; fxaddpar, primary_header, 'DAC1POL1', interpol_param(hk_table, 'NIT0E061', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC2POL1', interpol_param(hk_table, 'NIT0E062', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC1POL2', interpol_param(hk_table, 'NIT0E064', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC2POL2', interpol_param(hk_table, 'NIT0E065', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC1POL3', interpol_param(hk_table, 'NIT0E067', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC2POL3', interpol_param(hk_table, 'NIT0E068', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC1POL4', interpol_param(hk_table, 'NIT0E06A', date_avg, empty_params = empty_params)
		; fxaddpar, primary_header, 'DAC2POL4', interpol_param(hk_table, 'NIT0E06B', date_avg, empty_params = empty_params)

		fxaddpar, primary_header, 'TSENSOR', interpol_param(hk_table, 'NIT0E0E0', date_avg, empty_params = empty_params), '[degC] VLDA temperature'
		fxaddpar, primary_header, 'PMPTEMP', interpol_param(hk_table, 'NIT0L00D', date_avg, empty_params = empty_params), '[degC] PMP temperature'

		journal, 'Header keywords were calibrated using HK parameters:'
		journal, '  TSENSOR = ' + string(fxpar(primary_header, 'TSENSOR'), format = '(F0)')
		journal, '  PMPTEMP = ' + string(fxpar(primary_header, 'PMPTEMP'), format = '(F0)')
	endif

	if datatype eq 1 or datatype eq 4 or datatype eq 6 then begin
		fxaddpar, primary_header, 'HVU_SCR', interpol_param(hk_table, 'NIT0E070', date_avg, empty_params = empty_params), '[raw] HVU Screen commanded voltage'
		; CMDHVSCR e CMDHVMCP
		fxaddpar, primary_header, 'HVU_MCP', interpol_param(hk_table, 'NIT0E071', date_avg, empty_params = empty_params), '[raw] HVU MCP commanded voltage'
		fxaddpar, primary_header, 'HV_SCR_V', interpol_param(hk_table, 'NIT0E0B7', date_avg, empty_params = empty_params), '[V] HVU Screen + MCP read voltage', after = 'HVU_MCP'
		fxaddpar, primary_header, 'HV_MCP_V', interpol_param(hk_table, 'NIT0E0B6', date_avg, empty_params = empty_params), '[V] HVU MCP read voltage', after = 'HV_SCR_V'
		fxaddpar, primary_header, 'HV_MCP_I', interpol_param(hk_table, 'NIT0E0BF', date_avg, empty_params = empty_params), '[uA] HVU MCP current', after = 'HV_MCP_V'
		fxaddpar, primary_header, 'HV_TEMP', interpol_param(hk_table, 'NIT0E0B5', date_avg, empty_params = empty_params), '[degC] HVU temperature', after = 'HV_MCP_I'
		fxaddpar, primary_header, 'TSENSOR ', interpol_param(hk_table, 'NIT0E050', date_avg, empty_params = empty_params), '[degC] UVDA temperature'

		journal, 'Header keywords were calibrated using HK parameters:'
		journal, '  HVU_SCR  = ' + string(fxpar(primary_header, 'HVU_SCR'), format = '(F0)')
		journal, '  HVU_MCP  = ' + string(fxpar(primary_header, 'HVU_MCP'), format = '(F0)')
		journal, '  HV_SCR_V = ' + string(fxpar(primary_header, 'HV_SCR_V'), format = '(F0)')
		journal, '  HV_MCP_V = ' + string(fxpar(primary_header, 'HV_MCP_V'), format = '(F0)')
		journal, '  HV_MCP_I = ' + string(fxpar(primary_header, 'HV_MCP_I'), format = '(F0)')
		journal, '  HV_TEMP = ' + string(fxpar(primary_header, 'HV_TEMP'), format = '(F0)')
		journal, '  TSENSOR  = ' + string(fxpar(primary_header, 'TSENSOR'), format = '(F0)')
	endif

	if empty_params eq !null then empty_params = ''

	; replace verbose keyword values

	key = fxpar(primary_header, 'MEASKIND', count = count)
	if count gt 0 then begin
		pol_id = fxpar(primary_header, 'POL_ID')
		if key eq 0 and pol_id eq 0 then fxaddpar, primary_header, 'MEASKIND', 'Fixed pol.'
		if key eq 0 and pol_id ne 0 then fxaddpar, primary_header, 'MEASKIND', 'pB'
		if key eq 1 then fxaddpar, primary_header, 'MEASKIND', 'tB'
	endif

	key = fxpar(primary_header, 'FRAMEMOD', count = count)
	if count gt 0 then begin
		if key eq 0 then fxaddpar, primary_header, 'FRAMEMOD', 'Single'
		if key eq 1 then fxaddpar, primary_header, 'FRAMEMOD', 'Multiple'
	endif

	key = fxpar(primary_header, 'VLFPFILT', count = count)
	if count gt 0 then begin
		pol_id = fxpar(primary_header, 'POL_ID')
		if pol_id ne 0 then fxaddpar, primary_header, 'VLFPFILT', 'Not applicable' else begin
			if key eq 0 then fxaddpar, primary_header, 'VLFPFILT', 'Binning'
			if key eq 1 then fxaddpar, primary_header, 'VLFPFILT', 'Masking'
			if key eq 2 then fxaddpar, primary_header, 'VLFPFILT', 'No filter'
		endelse
	endif

	key = fxpar(primary_header, 'PMPSTAB', count = count)
	if count gt 0 then begin
		if key eq 0 then fxaddpar, primary_header, 'PMPSTAB', 'Not stable'
		if key eq 1 then fxaddpar, primary_header, 'PMPSTAB', 'Stable'
	endif

	key = fxpar(primary_header, 'REF_ROWS', count = count)
	if count gt 0 then begin
		if key eq 0 then fxaddpar, primary_header, 'REF_ROWS', 'Not included'
		if key eq 1 then fxaddpar, primary_header, 'REF_ROWS', 'Included'
	endif

	keys = ['PRESUM', 'CME_OBS', 'SUNDISK', 'CR_SEP', 'SP_NOISE', 'COMPR', 'MASKING', 'RADIAL']
	foreach key_name, keys do begin
		key = fxpar(primary_header, key_name, count = count)
		if count gt 0 then begin
			if key eq 0 then fxaddpar, primary_header, key_name, 'Disabled'
			if key eq 1 then fxaddpar, primary_header, key_name, 'Enabled'
		endif
	endforeach

	; remove unused keywords

	sxdelpar, primary_header, 'WIDTH'
	sxdelpar, primary_header, 'HEIGHT'
	sxdelpar, primary_header, 'X_SIZE'
	sxdelpar, primary_header, 'Y_SIZE'
	sxdelpar, primary_header, 'Z_SIZE'
	sxdelpar, primary_header, 'P_BANDS'
	sxdelpar, primary_header, 'N_BANDS'
	sxdelpar, primary_header, 'ORIG_X'
	sxdelpar, primary_header, 'ORIG_Y'

	; modify keywords for file history

	fxaddpar, primary_header, 'HISTORY', 'L1 FITS file created on ' + date

	; modify keywords for comments

	old_comment = fxpar(primary_header, 'COMMENT', count = count)
	if count eq 0 then old_comment = ''
	sxdelpar, primary_header, 'COMMENT'
	if max(old_comment.startswith('Warning: correction of the OBT for pB acquisitions was applied.')) then begin
		if ~ isa(comment) then comment = !null
		comment = ['Correction of the OBT for pB acquisitions was applied at L0 level.', comment]
	endif
	if max(old_comment.startswith('Warning: the OBT of the acquisition is missing.')) then begin
		if ~ isa(comment) then comment = !null
		comment = ['Warning: the OBT of the acquisition is missing.','  The generation time of the first science packet was used', '  to compute OBT_BEG. Polarimetric keywords DAC*POL*','  may be wrong.', comment]
	endif
	if isa(comment) then begin
		for k = 0, n_elements(comment) - 1 do $
			fxaddpar, primary_header, 'COMMENT', comment[k]
	endif

	; add checksum and datasum to the fits header

	fits_add_checksum, primary_header, data

	mwrfits, data, out_file_name, primary_header, /no_comment, /create, /silent

	journal, 'Fits file created:'
	journal, '  file name = ' + out_file_name

	; if applicable, save the data binary-table extension as it is

	if isa(data_bin_table) then mwrfits, data_bin_table, 'output/' + file_name, data_extension_header, /no_comment, /silent

	; build the telemetry extension

	hk_extension_header = !null
	fxaddpar, hk_extension_header, 'XTENSION', 'BINTABLE', 'Extension type'
	fxaddpar, hk_extension_header, 'BITPIX', 8, 'Number of bits per data pixel'
	fxaddpar, hk_extension_header, 'NAXIS', 2, 'Number of data axes'
	fxaddpar, hk_extension_header, 'NAXIS1', 0, 'Number of pixels along axis 1'
	fxaddpar, hk_extension_header, 'NAXIS2', 0, 'Number of pixels along axis 2'
	fxaddpar, hk_extension_header, 'PCOUNT', 0, 'Parameter count'
	fxaddpar, hk_extension_header, 'GCOUNT', 1, 'Group count'
	fxaddpar, hk_extension_header, 'EXTNAME', 'House-keeping', 'Extension name'

	hk_bin_table = make_bin_table(hk_table)

	mwrfits, hk_bin_table, out_file_name, hk_extension_header, /no_comment, /silent

	journal, '  HK binary-table extension correctly added'

	; unload the spice kernels

	cspice_unload, kernels

	journal, 'SPICE kernel files unloaded.'

	; write the auxiliary information file

	output = { $
		file_name: out_file_name, $
		l0_file_name: input.file_name, $
		log_file_name: 'output/metis_l1_prep_log.txt', $
		empty_params : empty_params[uniq(empty_params)]  $
 	}

	json_write, output, 'output/contents.json'

	journal, 'Output saved.'

	;close the log

	journal, 'Exiting without errors.'
	journal
	exit, status = 0

	error_handling:
	journal, 'Errors occurred while processing.'
	journal
	exit, status = 1
end