pro IRIS_PREP, iindex, idata, oindex, odata, $
	verbose = verbose, loud = loud, run_time = run_time, tdelt = tdelt, $
	version = version, only_version = only_version, strict = strict, $
	pstop = pstop, check = check, missing = missing, cubic = cubic, $
	spikefile = spikefile, despike_here = despike_here, update_roll = update_roll, $
	measure_fid = measure_fid, measure_wave = measure_wave, measure_aia = measure_aia, $
	write = write, logdir = logdir, dose = dose, ccdstat = ccdstat, $
	shift_fid = shift_fid, shift_wave = shift_wave, shift_aia = shift_aia, $
	filter_fid = filter_fid, filter_wave = filter_wave, filter_aia = filter_aia, $
	minbox = minbox, maxbox = maxbox, samebox = samebox, poly2d = poly2d, $
	nowarp = nowarp, nodark = nodark, noflat = noflat, nospat = nospat, $
	nobad = nobad, noback = noback, $
	sat_thresh = sat_thresh, nosat = nosat, desat = desat, nsatpix = nsatpix, $
	header_temps = header_temps, scaled = scaled, post_warp = post_warp, $
	nrt_pipeline = nrt_pipeline, _nrt_pipeline = _nrt_pipeline, pipeline = pipeline, $
	dont_filter_faint_fids = dont_filter_faint_fids, do_filter_faint_fids = do_filter_faint_fids, $
	ptest = ptest, kludge_fuv = kludge_fuv, noversion = noversion, $
	keyword_only = keyword_only, masks = masks, obsfile = obsfile, $
	fitchisq_max = fitchisq_max, _extra=_extra
	
;+
;
; NAME:
;   IRIS_PREP
;
; PURPOSE:
;	Convert IRIS level 1 images to level 1.5, including:
;		- Dark/pedestal removal and flat-fielding
;		- Replacement of spikes/bad pixels
;		- Geometric correction (rotation, translation, distortion, platescale)
;		- Wavelength correction (dispersion/shift)
;		- Update header keywords to reflect the above actions
;
; CATEGORY:
;   Image alignment
;
; SAMPLE CALLS:
;   Inputing file list:
;   IDL> IRIS_PREP, infiles, [0,1,2], oindex, odata
;   Inputing iindex and idata: 
;   IDL> IRIS_PREP, iindex, idata, oindex, odata
;
; INPUTS:
;   There are 2 basic usages for inputing the image and header data into IRIS_PREP:
;		= Case 1: Already read in the FITS files =
;	iindex	-	Array of structures containing FITS headers
;	idata	-	Array containing FITS image data
;		= Case 2: Just have the file names =
;	iindex	-	Array of strings giving path/filename for FITS files to read
;	idata	-	integer array of indices to specify which filenames in iindex should
;				be read (defaults to all)
;
; OUTPUTS (OPTIONAL):
;   oindex - The updated index structure of the input image(s)
;   odata  - Prepped output image(s).
;
; KEYWORDS:
;	/pstop	-	This program brakes (breaks?) for debugging
;	/check	-	Display a window showing the warped data with the transformed ROIs
;				superimposed (passed through to IRIS_PREP_GEOWAVE_CORRECT)
;	/strict	-	If set, then bail out if a non-lev1 input is given or other unexpected
;				funniness is detected. Also, when bailing out, set the output 
;				index to the input index, and the output data to NaNs
;	/run_time	-	Print out the time taken to complete
;	tdelt	-	Blank variable that returns the elapsed run time (in seconds)
;	nsatpix	-	Blank variable that returns the number of saturated pixels
;	sat_thresh-	Number of DN to consider a pixel saturated (default is 1.6e4)
;	/verbose-	Print some extra stuff
;	/loud	-	Super verbose (passed through to IRIS_PREP_ALIGN_IMAGE)
;	/maxbox	-	If set, then transformed ROIs are re-sized to include all valid data
;				This is the default behavior; if something else is desired, set either
;				/minbox or /samebox
;	/minbox	-	If set, then transformed ROIs are re-sized to exclude any missing data.
;	/samebox	-	If set, then transformed ROIs are mapped to the same size as the 
;					input ROIs (not generally a good idea since they may have moved)
;	/nowarp	-	If set, then do not apply any warping to the image
;	/nobad	-	If set, then do not set permanently bad pixels (dust) to 0
;	/nosat	-	If set, then do not set saturated pixels to Inf
;	/desat	-	If set, then replace saturated pixels with a large finite value
;	/noflat	-	If set, then do not apply flatfielding
;	/nospat	-	If set, then do not apply the spatially-varying flatfield correction
;				to spectra
;	/nodark	-	If set, then do not subtract dark/pedestal
;	/noback	-	If set, then do not subtract visible scattered light background
;				from FUV spectra
;	_extra	-	Passed through to READ_IRIS
;	spikefile	-	Can be set as a switch (/spikefile) to look for the spike file
;					in the local (LMSAL) tree, or can be set to a string giving
;					the path and filename to the spikes file. A spikes file is a
;					FITS file describing the spikes found during pipeline processing
;					of each image. If set, then the spikes are corrected.
;	despike_here	-	If set as a switch, then iris_prep_despike is called at
;						run time to correct spikes
;	missing	-	Can be set to a value that is used to indicate missing data. Defaults
;				to NaN (so set this to 0 or something like that if you don't like NaNs)
;	/scaled -	if set, then the output is converted to scaled integers using
;				iris_prep_float2int
;	/measure_fid	-	Set if you want to run IRIS_PREP_FID_FINDER to find the 
;					location of the fiducials and write it to a file
;	/measure_wave -	Set if you want to run IRIS_PREP_WAVECORR to find the 
;					location of the Ni I NUV line and write it to a file
;	/measure_aia -	Set if you want to run IRIS_AIA_CORR to find the offset
;					between the IRIS slitjaw image and the nearest corresponding
;					AIA/HMI image (results are written to 
;	/write	-	set to allow measure_fid, measure_wave and measure_aia to write 
;				to external files (specified by logdir)
;	logdir=	-	The path to an area where output logs and trending information 
;				should be written. 
;	/shift_fid	-	Set if you want to apply the time- and temperature-dependent
;					shift to put the fiducials in their nominal positions. 
;	/shift_wave	-	Set if you want to apply the time- and temperature-dependent
;					shift to put the wavelengths in	their nominal positions. 
;	/shift_aia	-	Set if you want to apply the updates to the WCS information 
;					in the header determined by cross-correlation with SDO. IF
;					/measure_aia is set, then the correction is from the real-time
;					measurements of this image; otherwise, it is loaded from the
;					side database
;	/header_temps-	Set if you want to use only the temperatures in the header (not
;					currently a complete set); by default, temperatures are looked
;					up at runtime using iris_time2hk
;	/update_roll-	Set if you want to update the header SAT_ROT, OPHASE and
;					temperature values using iris_time2hk; by default, the header
;					values are used (except for those temperatures not set in the
;					level 1 header, which are always looked up)
;	/post_warp	-	Set if you want to measure the fiducial and wavelength shift
;					after warping; by default, they are measured before warping
;	/keyword_only-	Set if you want to produce only an output header, not an output
;					image (much faster...)
;	obsfile=	-	Set to the name of the genx file with all the per-image fits of fiducial
;					position and wavelength are stored; if not set, then it is
;					looked up from the date directories in /irisa/data/prep/
;
;	/pipeline	-	If set, then assuming it is running on the definitive data
;					in the pipeline, and set keywords appropriately
;	/nrt_pipeline -	If set, then assume it is running on the NRT data in the 
;					pipeline, and set keywords appropriately
;	/_nrt_pipeline-	Synonym for nrt_pipeline
;	/ptest		-	If set, then do some things differently (changes depending
;					on what is being debugged)
;	/kludge_fuv -	Put in a very crude fix to correct for pedestal quadrant offsets
;					by subtracting out the median of the lower half of the data
;					values in each quadrant
;	/noversion	-	If set (and keyword_only is set), then do not look up
;					versions of the flat, dark, background subtraction and bad
;					pixel map
;	fitchisq_max -	Passed through to iris_prep_align_image
;	/dont_filter_faint_fids -	If set, then /filter_fid is overriden for the FUV SJI.
;								Note that this is set by the /pipeline keyword 
;	/do_filter_faint_fids -	If set (along with /pipeline), then /dont_filter_faint_fids 
;							is overriden and the fiducial trend data is applied to all
;							channels. (Don't use unless setting /pipeline)
;
; WRITTEN:
;	P.Boerner 2013/06 boerner ~ at ~ lmsal ~ dot ~ com
;
; HISTORY:
;	See https://www.lmsal.com/iris_science/test?cmd=view-logbook&test_id=TNCIRISCI2
;
;-


;++++++++++++++++++++++++++++++++++++
; 0. Set up:						;
;	Define some defaults, 			;
;	Check inputs for consistency	;
;------------------------------------

; Set up defaults for keywords and constants
t0 = SYSTIME(/sec) 
run_time = KEYWORD_SET(run_time)
verbose = KEYWORD_SET(verbose)
loud 	= KEYWORD_SET(loud)
strict	= KEYWORD_SET(strict)
nodark	= KEYWORD_SET(nodark)
nowarp	= KEYWORD_SET(nowarp)
nospat	= KEYWORD_SET(nospat)
header_temps = KEYWORD_SET(header_temps)
poly2d = KEYWORD_SET(poly2d)
if not KEYWORD_SET(pstop) then pstop = 0

; Define version variables
;progver = 'V1.0' ; 2013-02-10 (PB)
;progver = 'V1.1' ; 2013-07-18 (PB)
;progver = 'V1.2' ; 2013-08-26 (PB)
;progver = 'V1.3' ; 2013-08-31 (PB)
;progver = 'V1.4' ; 2013-09-19 (PB)
;progver = 'V1.5' ; 2013-09-26 (PB)
;progver = 'V1.6' ; 2013-09-30 (PB)
;progver = 'V1.7' ; 2013-10-02 (PB)
;progver = 'V1.8' ; 2013-10-03 (PB)
;progver = 'V1.9' ; 2013-10-11 (PB)
;progver = 'V1.10' ; 2013-10-14 (PB)
;progver = 'V1.11' ; 2013-10-15 (PB)
;version = '1.12' ; 2013-10-16 (PB)
;version = '1.121'; 2013-10-16 (SLF)
;version = '1.13'; 2013-10-17 (PB)
;version = '1.14'; 2013-10-23 (PB)
;version = '1.15'; 2013-10-24 (PB)
;version = '1.16'; 2013-10-25 (PB)
;version = '1.17'; 2013-11-01 (PB)
;version = '1.18'; 2013-12-04 (PB)
;version = '1.19'; 2013-12-13 (PB)
;version = '1.20'; 2014-01-17 (PB)
;version = '1.21'; 2014-02-18 (PB)
;version = '1.22'; 2014-03-06 (PB)
;version = '1.23'; 2014-03-07 (PB)
;version = '1.24'; 2014-03-27 (PB)
;version = '1.25'; 2014-04-03 (PB)
;version = '1.26'; 2014-04-17 (PB)
;version = '1.27'; 2014-07-07 (PB)
;version = '1.28'; 2014-08-28 (PB)
;version = '1.29'; 2014-09-24 (PB)
;version = '1.30'; 2014-09-24 (PB)
;version = '1.31'; 2015-01-12 (PB)
;version = '1.32'; 2015-02-10 (PB)
;version = '1.33'; 2015-03-17 (PB)
;version = '1.34'; 2015-03-23 (PB)
;version = '1.35'; 2015-04-10 (PB)
;version = '1.36'; 2015-05-27 (PB)
;version = '1.37'; 2015-06-01 (PB)
;version = '1.38'; 2015-06-12 (PB)
;version = '1.39'; 2015-06-26 (PB)
;version = '1.40'; 2015-07-10 (PB)
;version = '1.41'; 2015-07-13 (PB)
;version = '1.42'; 2015-07-15 (PB)
;version = '1.43';  2015-10-12 (SF) ; per PB, default option/kw settings for /NRT_PIPELINE
;version = '1.44';  2015-11-04 (RPT) - marking dark and calibration updates; no code changes relative to 1.43
;version = '1.45';  2015-12-18 (RPT) - marking flat updates, again no code change vs 1.43/44
;version = '1.46';  2015-12-21 (RPT) - retroactive NUV flat updates w/better darks for Sarah's whole set.  
;version = '1.47';  2016-01-05 (RPT) - new flats 12/30/15
;version = '1.48'; 2016-02-03 (RPT) - marking installing dark updates (iris_make_dark from 11/25/15, iris_dark_trend_fix from 1/10/16)
;version = '1.49';  2016-02-08 (RPT, with Wei) - marking flat updates from 2016/01/27
;version = '1.50';  2016-03-13 (Wei Liu) - updated flats from 2016/02/24, fuv background from 2016/02/22, done by Sean Brannon (handed over by Sarah Jaeggli, 2016/02/29-03/04; Sean finished 03/11, Friday)
; version = '1.51';  2016-04-20 (Wei Liu) - updated 20160312_220808_FUV_background, flat_NUV_SPATIAL_20160327_120040, flat_SJI_*_20160323, from Sean Brannon (done on 2016/04/18)
;version = '1.52'; 2016-05-05 (RPT) - cloned flat fields & placed with fake times adjacent to bakeouts in Oct. 2014 and Oct 2015, so that pipeline will use the appropriate pre/post bakeout flat
;version = '1.53'; 2016-05-18 (RPT cleaning up after Wei) - new iris_dark_trend_fix from S. Saar, now with proper name - progver = 'v2016.May.13' ;--- (SSaar) V6 update of double sine model + quad
                 ; trend, P2=P1/2, data thru 05/16 
;version = '1.54'; 2016-06-10 (Wei Liu) - marking SJI flat updates from 2016/04/20 and 2016/05/06, as well as FUV background from 2016/04/10 and 2016/05/08; no sg flats yet, wait for Sean B. updates
;version = '1.55'; 2016-07-01 (Wei Liu) - marking updates: FUV background - 20160605; NUV SG Spatial flats - 20160327, 20160420, 20160507, 20160616; SJI flat - 20160615, after Sean B.'s recent updates.
;version = '1.56';2016-07-06 (RPT) - Marking flats (both SJI and SG) 20160518-0519.  Also covers pre/post bakeout cloning of 20160427 (copying the before/after flats to 0427_000000 and 0428_000000)
;version = '1.57'; 2016-08-19 (Wei Liu) - marking updates from Sean: FUV background - 20160703; NUV SG Spatial flats - 20160715; SJI flat - 20160715-20160716
;version = '1.58'; 2016-08-24 (Wei Liu) - marking updates from Sean: FUV background - 20160801; NUV SG Spatial flats - 20160810; SJI flat - 20160810
;version = '1.59'; 2016-09-08 (Wei Liu) - upaded FUV background - 201608027 from Sean
;version = '1.60'; 2016-09-13 (Wei Liu) - upaded NUV SG Spatial and SJI flats - 20160907 from Sean
;version = '1.61'; 2016-9-14 (RPT) - converted the bad pixel maps to .geny (savegenx/restgenx) methods because they were large enough to crash ultra/solserv
                                ; redid the badpixel maps from
                                ; yesterday's flat up date in
                                ; new format. Should not be any real
                                ; difference in data but marking regardless
;version = '1.62'; 2016-10-07 (Wei Liu) - new iris_dark_trend_fix from Steve Saar, progver = 'v2016.Oct.07' ;--- (SSaar) V7 update of 2 sine model + shifted quad trend, P2=P1/2, data thru 09/16
;version = '1.63'; 2016-10-13 (Wei Liu) - marking updates from Sean: FUV background - 20160926; NUV SG Spatial flats - 20161005; SJI flat - 20161005
;version = '1.64'; 2016-10-28 (JP Wuesler) - new iris_prep_align_image has the real change, correct bug in fiducial shifting, now decides good fit/applies shift separately in X and Y axes
;version = '1.65'; 2016-11-16 (Wei Liu) - marking updates from Sean Brannon: FUV background taken on 2016-10-22; NUV SG Spatial flat and SJI flats taken on 2016-11-02
;version = '1.66'; 2016-11-18 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2016.Nov.14' ;--- (SSaar) V8 same as V7, fixed indexing bug
;version = '1.67'; 2016-12-09 (Wei Liu) - marking updates from Sean Brannon: (no FUV background due to eclipse season); NUV SG Spatial flat from 2016-12-01 and SJI flats from 2016-12-02
;version = '1.68'; 2016-12-28 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2016.Dec.28' ;--- (SSaar) V9 update (NUV only) of double sine model, +linear trend, P2=P1/2, data thru 12/16
;version = '1.69'; 2017-01-18 (Wei Liu) - marking updates from Sean Brannon: (no FUV background due to eclipse season); NUV SG Spatial flat from 2016-12-28 and SJI flats from 2016-12-29
;version = '1.70'; 2017-01-30 (Ryan Timmons) - change to iris_time2hk for temperatures, using the /irisa/data/prep/aux/temp_interpolated folder.  
;version = '1.71'; 2017-02-10 (Wei Liu) - marking updates from Sean Brannon: (no FUV background due to eclipse season); NUV SG Spatial flat from 2017-01-27 and SJI flats from 2016-01-26
                 ;--- Notes by Wei Liu 2017-03-13: restored the original version 1.71 comments above, disregard the following two lines of comments about the test version 1.71 which was never released to SSW --------
                 ;version = '1.71' ; 2017-01-31 (Wei Liu) - special version for testing Martin W.'s double precision fits header code.
                 ;EDIT 1.71 became a real version for Jan 26-27 2017 flatfields sooo
;version = '1.72'                ; ; 2017-02-21 (Ryan Timmons) official version of Martin's double precision kewyords/header + updated FUV1/2 wavelength offset, paths chagned:
                 ;/archive/ssw/iris/idl/uio/iris_simulator/irissim_constants__define.pro
                 ;/archive/ssw/site/idl/iris/irisl12_getkeywords.pro
                 ;/archive/ssw/iris/idl/lmsal/calibration/iris_mk_pointdb.pro
                 ;/archive/ssw/iris/idl/uio/level1to2/iris_level1to2.pro  (also just a
                 ;version/date stamping)
;version = '1.73'; 2017-02-24 (Ryan Timmons) - doh, had onlining issues with the two uio paths in 1.72.  This just marks correcting those.  
;version = '1.74'; 2017-03-06 (Ryan Timmons) - still more issues, finally solved with Viggo/Sam/Martin..so this is really the official online of double precision header/keyword splus the FUV1/2 offset
;version = '1.75'; 2017-03-13 (Wei Liu) - marking updates from Sean Brannon: FUV background taken on 2017-02-26; NUV SG Spatial flat and SJI flats taken on 2017-02-24/25
;version = '1.76'; 2017-03-28 (Wei Liu) - marking updates from Sean Brannon: NUV SG Spatial flat and SJI flats taken on 2017-03-22
;version = '1.77'; 2017-04-10 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2017.Apr.07' ;--- (SSaar) V10 update of double sine model +quad trend, P2=P1/2, data thru 03/17 (also typo fix from "+linear" to "+quad" in progver = 'v2016.Dec.28' comment line)
;version = '1.78'; 2017-04-18 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-04-09, NUV SG Spatial flat and SJI flats from 2017-04-05; also automated the process for ingesting these updates (revised my IDL routines).
;version = '1.79'; 2016-08-29 (J-P Wuelser) - fixed bug causing filter_* to be ignored when called with filename,indices instead of index,data, if indices had single element
                 ; 2017-02-28 (J-P Wuelser) - changing lvl_num of input in 2nd call to iris_prep_align image
                 ; 2017-04-20 (J-P Wuelser) - also with v.1.79: updated iris_mk_pointdb.pro to v.10 & upgrade of iris_isp2wcs.pro
                 ; 2017-04-24 (J-P Wuelser) - also with v.1.79: tweaked iris_prep_wavecorr.pro & iris_prep_filter_wave.pro
;version = '1.80' ; 2017-05-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-05-07, NUV SG Spatial flat and SJI flats from 2017-05-03
;version = '1.81';  2017-05-19 (Ryan Timmons) - marking updates from Sean Brannon: FUV background from 2017-05-07  (redone due to data recovery from a bad pass after the first one).  Also contains JP's fix for the dose logging although that should not directly affect pipeline results.  
;version = '1.82' ; 2017-06-09 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-06-04, NUV SG Spatial flat and SJI flats from 2017-05-31.
;version = '1.83' ; 2017-06-12 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2017.Jun.06' ;--- (SSaar,JPrchlik) V11 update of double sine model +quad trend, P2=P1/2, data thru 05/17
;version = '1.84' ; 2017-07-07 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-07-02, NUV SG Spatial flat and SJI flats from 2017-06-28/29.
;version = '1.85' ; 2017-08-07 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-07-30, NUV SG Spatial flat and SJI flats from 2017-07-26/27.
;version = '1.86' ; 2017-09-01 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-08-27, NUV SG Spatial flat and SJI flats from 2017-08-24.
;version = '1.87' ; 2017-10-02 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-09-25, NUV SG Spatial flat and SJI flats from 2017-09-20.
;version = '1.88' ; 2017-10-17 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2017.Oct.16' ;--- (SSaar,JPrchlik) V12 update of double sine model +quad trend, P2=P1/2, data thru 10/17
;version = '1.89' ; 2017-10-25 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2017-10-20, NUV SG Spatial flat and SJI flats from 2017-10-18.
;version = '1.90' ; 2017-11-21 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2017-11-15/16.
;version = '1.91' ; 2017-12-14 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2017.Dec.14' ;--- (SSaar,JPrchlik) V13 update of double sine model +quad trend (now with stop time for FUV), P2=P1/2, data thru 11/17
                  ; Jakub/Steve recommended reprocessing data after 2017-Aug-9
;version = '1.92' ; 2017-12-18 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2017-12-13/14.
;version = '1.93' ; 2018-01-19 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2018-01-10.
;version = '1.94' ; 2018-02-06 (Wei Liu) - new iris_dark_trend_fix from Steve Saar: progver = 'v2018.Feb.02' ;--- (SSaar,JPrchlik) V14 update of double sine model +quad trend (now with stop time), P2=P1/2, data thru 01/18; recommended data reprocessing starting Nov. 1, 2017
;version = '1.95' ; 2018-02-15 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2018-02-07/08.
;version = '1.96' ; 2018-03-14 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/03/10, NUV SG Spatial flat and SJI flats from 2018/03/07.
;version = '1.97' ; 2018-04-12 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/04/08, NUV SG Spatial flat and SJI flats from 2018/04/04-05.
;version = '1.98' ; 2018-05-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/05/06, NUV SG Spatial flat and SJI flats from 2018/05/02.
;version = '1.99' ; 2018-06-07 (Wei Liu) - (1)     updates from Sean Brannon: FUV background from 2018/06/03, NUV SG Spatial flat and SJI flats from 2018/05/30-31.
                  ;                        (2) new iris_dark_trend_fix from Steve Saar: progver = 'v2018.May.29': 
                  ;--- (SSaar,JPrchlik) V15 update of double sine model +quad trend, P2=P1/2, data thru 05/18;  linear+quad trend now reduced after 8/17
;version = '2.00' ; 2018-07-05 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/07/01, NUV SG Spatial flat and SJI flats from 2018/06/27.
                  ; also made duplicates of the 2018-06-07 update to have time-stamps of 20180613_170000, and of today's update to have timestamps of 20180615_000000, right before and after the bakeout
                  ; to make sure the pipleline grab the calibration files from the same side of the bakeout nearest in time for the data to be processed.
;version = '2.01' ; 2018-08-03 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/07/29, NUV SG Spatial flat and SJI flats from 2018/07/25-26.
;version = '2.02' ; 2018-08-31 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/08/24, NUV SG Spatial flat and SJI flats from 2018/08/22.
;version = '2.03' ; 2018-09-26 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/09/21, NUV SG Spatial flat and SJI flats from 2018/09/19.
;version = '2.04' ; 2018-10-18 (Wei Liu) - new iris_dark_trend_fix from Jakub Prchlik/Steve Saar: progver = 'v2018.Oct.17' ;--- (SSaar,JPrchlik) V16 update of double sine model+quad trend, P2=P1/2, data thru 05/18, linear+quad trend now reduced after 8/17, fractional drop in offset and increase in quadratic term following the 6/18 bakeout;
                  ; recommended data reprocessing since 2018-Jun-15, after the 2018-Jun-13 to 14 CCD bakeout.
;version = '2.05' ; 2018-10-29 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2018/10/24, NUV SG Spatial flat and SJI flats from 2018/10/16.
;version = '2.06' ; 2018-12-21 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2018/12/15-16.
;version = '2.07' ; 2019-01-10 (Wei Liu) - new iris_dark_trend_fix from Jakub Prchlik/Steve Saar, progver = 'v2019.Jan.10' ;--- (SSaar,JPrchlik) V17 update of double sine model....
;version = '2.08' ; 2019-01-16 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2019/01/09.
;version = '2.09' ; 2019-01-23 (Wei Liu) - new iris_dark_trend_fix from Jakub Prchlik/Steve Saar, improved temporary fix: progver = 'v2019.Jan.22' ;--- (SSaar,JPrchlik) V18 update of double sine model...
;version = '2.10' ; 2019-02-20 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c of eclipse season, NUV SG Spatial flat and SJI flats from 2019/02/06.
;version = '2.11' ; 2019-03-15 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/02/27, NUV SG Spatial flat and SJI flats from 2019/03/06-07.
;version = '2.12' ; 2019-04-09 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/03/31, NUV SG Spatial flat and SJI flats from 2019/04/03.
;version = '2.13' ; 2019-04-30 (Wei Liu) - new iris_dark_trend_fix from SAO: progver = 'v2019.Apr.26' ;--- (VPolito,JPrchlik,SSaar) V19
;version = '2.14' ; 2019-05-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/04/28, NUV SG Spatial flat and SJI flats from 2019/05/01-02.
;version = '2.15' ; 2019-06-06 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/05/26, NUV SG Spatial flat and SJI flats from 2019/05/29.
;version = '2.16' ; 2019-07-03 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/06/23, NUV SG Spatial flat from 2019/06/29 and SJI flats from 2019/06/26.
;version = '2.17' ; 2019-07-29 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/07/20, NUV SG Spatial flat and SJI flats from 2019/07/24.
;version = '2.18' ; 2019-08-30 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/08/17, NUV SG Spatial flat and SJI flats from 2019/08/21.
;version = '2.19' ; 2019-09-24 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/09/15, NUV SG Spatial flat and SJI flats from 2019/09/17.
;version = '2.20' ; 2019-10-27 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2019/10/14, NUV SG Spatial flat and SJI flats from 2019/10/16-17.
;version = '2.21' ; 2019-11-12 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2019.Oct.30' ;--- (Guliano) V20 (FUV1,2,3, 4 and NUV 2, 3, 4): refit all model parameters.
;version = '2.22' ; 2019-11-19 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2019/11/13.
;version = '2.23' ; 2019-12-17 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2019/12/11.
;version = '2.24' ; 2020-01-19 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2020/01/08-09.
;version = '2.25' ; 2020-02-04 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2020.Jan.22' ;--- (Guliano) V21 (FUV 2 and 4, NUV3)
;version = '2.26' ; 2020-02-17 (Wei Liu) - marking updates from Sean Brannon: no FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2020/02/05.
;version = '2.27' ; 2020-03-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/03/01 (1st one after the recent eclipse season), NUV SG Spatial flat and SJI flats from 2020/03/04-05.
;version = '2.28' ; 2020-04-11 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/03/29, NUV SG Spatial flat and SJI flats from 2020/04/01.
;version = '2.29' ; 2020-04-27 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2020.April.21' ;--- (Guliano) V22 (FUV1,2,3,and 4, NUV1,3 and 4): refit all parameters for all channgels except NUV2
;version = '2.30' ; 2020-04-28 (Ryan Timmons) - merging in edits to this file for JP Wuelser/Paul Boerner work on applying the IRIS-AIA correlation updates to the pointing keywords.  Includes updates to iris_aia_corr, iris_align_aia, iris_prep_filter_aia, iris_prep_filter_obs, and irisl12_shiftaia
;version = '2.31' ; 2020-05-08 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/04/26, NUV SG Spatial flat and SJI flats from 2020/04/29.
;version = '2.32' ; 2020-05-13 (Paul Boerner) - Adding dont_filter_faint_fids keyword
;version = '2.33' ; 2020-06-09 (Ryan Timmons) - online iris_mk_pointdb v11 (from JP Wuelser) - significant improvements to fallback solutions for fiducial, wavelength calibrations.
;iris_prep now defaults to *not* using the fiducial fits for the FUV SJI, as they have rarely worked correctly since 2015. The fallback solution should give equal
;or superior performance for the whole mission. 
;version = '2.34' ; 2020-06-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/05/25, NUV SG Spatial flat and SJI flats from 2020/05/27-28.
;version = '2.35' ; 2020-07-02 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/06/20, NUV SG Spatial flat and SJI flats from 2020/06/24.
;version = '2.36' ; 2020-08-02 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/07/19, NUV SG Spatial flat and SJI flats from 2020/07/22-23.
;version = '2.37' ; 2020-08-28 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2020.August.26' ;--- (Guliano) V23 (FUV1,2,3,and 4, NUV1,3 and 4): refit Scale, OffDrop, and OffNSop parameters for all channgels except NUV2 to account for the continued over estimation from the model in these 7 channels. 
;version = '2.38' ; 2020-09-07 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2020/08/15 (onlined 2020/09/01), NUV SG Spatial flat and SJI flats from 2020/08/19 (onlined today, 2020/09/07).
;version = '2.39' ; 2020-10-20 (Wei Liu) - marking combo updates from Sean Brannon: FUV background from 2020/09/13 and 10/13, NUV SG Spatial flat and SJI flats from 2020/09/16 and 10/14
;version = '2.40' ; 2020-11-18 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2020/11/12
;version = '2.41' ; 2020-12-15 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2020/12/09-10
;version = '2.42' ; 2021-01-11 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2021/01/06-07
;version = '2.43' ; 2021-01-12 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2021.January.12' ;--- (Guliano) V24 (FUV1,2,4, and NUV3): refit Amp1, Amp2, and Scale for 4 channels to account for the drop due to eclipse season
;version = '2.44' ; 2021-02-16 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2021/02/03
;version = '2.45' ; 2021-03-09 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/02/28, NUV SG Spatial flat and SJI flats from 2021/03/03.
;version = '2.46' ; 2021-04-26 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/03/27, NUV SG Spatial flat and SJI flats from 2021/03/31.
;version = '2.47' ; 2021-04-27 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: 'v2021.Apr.27' ;--- (Guliano) V25 (FUV1,2,3,and 4, NUV1,3 and 4)
;version = '2.48' ; 2021-05-12 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/04/25, NUV SG Spatial flat and SJI flats from 2021/04/28.
;version = '2.49' ; 2021-06-04 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/05/23, NUV SG Spatial flat and SJI flats from 2021/05/26.
;version = '2.50' ; 2021-07-15 (Wei Liu) - 1) marking updates from Sean Brannon: FUV background from 2021/06/20, NUV SG Spatial flat and SJI flats from 2021/06/23-24.
                  ;  2) new iris_dark_trend_fix.pro from SAO: 'v2021.Jul.14' ;--- (Guliano) V26 (All Ports)
;version = '2.51' ; 2021-07-30 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/07/18, NUV SG Spatial flat and SJI flats from 2021/07/21.
;version = '2.52' ; 2021-08-24 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/08/15, NUV SG Spatial flat and SJI flats from 2021/08/18-19.
;version = '2.53' ; 2021-09-21 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/09/12, NUV SG Spatial flat and SJI flats from 2021/09/15.
;version = '2.54' ; 2021-10-21 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2021/10/10, NUV SG Spatial flat and SJI flats from 2021/10/13-14.
;version = '2.55' ; 2021-11-12 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: 'v2021.Nov.10' ;--- (Guliano) V27: All ports were refit following continued overestimates and consistent darks.
;version = '2.56' ; 2021-11-20 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2021/11/10.
;version = '2.57' ; 2021-11-22 (Ryan Timmons) - marking a fix from Martin affecting some of the new high-cadence flare observations and fixing the FOV bug.  
;version = '2.58' ; 2021-12-24 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2021/12/08-09.
;version = '2.59' ; 2022-01-14 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2022/01/05
;version = '2.60' ; 2022-01-21 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: 'v2022.January.14' ;--- (Guliano) V28 (All Ports): All ports were refit following continued overestimates.
;version = '2.61' ; 2022-02-11 (Wei Liu) - marking updates from Sean Brannon: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2022/02/02.
;version = '2.62' ; 2022-03-09 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2022/02/27 (1st one after the eclipse season), NUV SG Spatial flat and SJI flats from 2022/03/03.
;version = '2.63' ; 2022-04-11 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2022/03/26, NUV SG Spatial flat and SJI flats from 2022/03/29.
;version = '2.64' ; 2022-05-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2022/04/24, NUV SG Spatial flat and SJI flats from 2022/04/27.
;version = '2.65' ; 2022-06-10 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2022/05/22, NUV SG Spatial flat from 2022/05/25, and SJI flats from 2022/05/28.
;version = '2.66' ; 2022-07-27 (Wei Liu) - marking updates from Sean Brannon: FUV background from 2022/06/19, NUV SG Spatial flat from 2022/06/22, and SJI flats from 2022/06/22.
;version = '2.67' ; 2022-08-01 (Wei Liu) - 1) marking updates from Sean Brannon: FUV background from 2022/07/17, NUV SG Spatial flat from 2022/07/20, and SJI flats from 2022/07/20.
                  ;  2) new iris_dark_trend_fix.pro from SAO: progver = 'v2022.Jul.22' ;--- (Guliano) V29 (All Ports): MAJOR CHANGE TO DARK MODEL.
;version = '2.68' ; 2022-09-14 (Wei Liu) - 1) marking updates from Sean Brannon: FUV background from 2022/08/13, NUV SG Spatial flat and SJI flats from 2022/08/17.
                  ;  2) Note: this is the first flat update since the relocation of all calibration files from $SSW/iris/data to $SSWDB/iris/data (made on 2022/08/10 by Ryan Timmons).
;version = '2.69' ; 2022-11-12 (Wei Liu) - 1) marking updates from Sean Brannon and Chunming Zhu, FUV background from 2022/09/11 and 10/08, NUV SG Spatial flat and SJI flats from 2022/09/14 and 10/13. Delay mainly due to changes of hands (from Sean Brannon to Chunming Zhu).
;version = '2.70' ; 2023-01-25 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2023.Jan.20' ;--- (Guliano) V30 (All Ports): Model C was created to cover data from 2022.
;version = '2.71' ; 2023-06-02 (Wei Liu) - 1) marking updates from Chunming Zhu @MSU: FUV background from 2023/02-2023/04, NUV SG Spatial flat from 2022/11-2023/04, and SJI flats from 2022/11-2023/04.
                  ;  2) new iris_dark_trend_fix.pro from SAO: 'v2023.June.01' ;--- (Guliano) V31 (All Ports); iris data reprocessing from 2022/10/25 to date was recommended for both flat/dark updates made today. 
;version = '2.72' ; 2023-06-05 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2023/05/20, NUV SG Spatial and SJI flats from 2023/05/24.
;version = '2.73' ; 2023-07-20 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2023/06/18, NUV SG Spatial and SJI flats from 2023/06/21.
;version = '2.74' ; 2023-08-14 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2023.Aug.11' ;--- (Guliano) V32 (All Ports): Minor adjustments to all ports due to larger than expected decrease. 
;version = '2.75' ; 2023-08-21 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2023/07/17, NUV SG Spatial and SJI flats from 2023/07/19 to 07/21.
;version = '2.76' ; 2023-08-23 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2023/08/13, NUV SG Spatial and SJI flats from 2023/08/16 to 08/18.
;version = '2.77' ; 2023-10-22 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2023/09/12 and 2023/10/09, NUV SG Spatial and SJI flats from 2023/09/13-14 and 2023/10/11.
;version = '2.78' ; 2023-12-20 (Wei Liu) - marking updates from Chunming Zhu @MSU: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2023/11/08 and 2023/12/06.
;version = '2.79' ; 2024-01-25 (Wei Liu) - marking updates from Chunming Zhu @MSU: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2024/01/04.
;version = '2.80' ; 2024-01-26 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2024.Jan.10' ;--- (Guliano) V33 (All Ports): Improved all fit parameters of all ports to match the downward trend of the fit.
;version = '2.81' ; 2024-02-10 (Wei Liu) - marking updates from Chunming Zhu @MSU: no FUV background (eclipse season), NUV SG Spatial flat and SJI flats from 2024/01/31.
;version = '2.82' ; 2024-03-13 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2024/02/25 calib run, NUV SG Spatial flat and SJI flats from 2024/02/28 calib run.
;version = '2.83' ; 2024-04-04 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2024.April.01' ;--- (Guliano) V34 (All Ports): Model D locked in for data 2022/11 through 2023/12; 
                  ; plan to start reprocessing from mid-Oct 2022 to diagnose the FUV SG jump found on 2022-Oct-26
;version = '2.84' ; 2024-05-14 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2024/03/24 and 2024/04/21, NUV SG Spatial flat and SJI flats from 2024/03/26-27 and 2024/04/24.
;version = '2.85' ; 2024-08-04 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2024/05/18, 06/16, 07/16, NUV SG Spatial flat and SJI flats from 2024/05/23, 06/19-20, 07/17-18.
; version = '2.86' ; 2024-08-06 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2024.August.06' ;--- (Guliano) V35 (All Ports): Update of model to improve fit Utilizes data from 2023 and 2024 for model generation, not reproecessing needed/recommended.
;version = '2.87' ; 2024-08-30 (Ryan Timmons) - test version to use the new iris_prep_get_back2 from JPWuelser, ONLY on pre 2023 data.  Idea is this online a few days to run a test set of obs.
;version = '2.88' ; 2024-09-10 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2024/08/12, NUV SG Spatial flat and SJI flats from 2024/08/14
;version = '2.89' ; 2024-10-26 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2024/09/08, 10/05, NUV SG Spatial flat and SJI flats from 2024/09/12-13, 10/09-10
;version = '2.90' ; 2025-01-20 (Wei Liu) - updates after long delay partly due to JSOC outage since 2024-Nov-26:
                  ; 1) new flats from Chunming Zhu @MSU: No FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2024/11/06, 2024/12/04, 2025/01/01;
                  ; 2) new iris_dark_trend_fix.pro from Lucas Guliano @SAO: 'v2025.January.08', V36 (All Ports): Update of model to improve fit, Temporary bridge during JSOC outage.
;version = '2.91' ; 2025-02-23 (Wei Liu) - marking updates from Chunming Zhu @MSU: No FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2025/01/29-01/30.
;version = '2.92' ; 2025-03-07 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/02/23, NUV SG Spatial flat and SJI flats from 2025/02/26.
;version = '2.93' ; 2025-03-21 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2025.March.18', (Guliano) V37: Model E locked in for data [2024/01 - 2024/10/31], recommended data reprocessing for this period.
;version = '2.94' ; 2025-05-03 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/03/23 & 04/20, NUV SG Spatial flat and SJI flats from 2025/03/26-27 & 04/23-24
;version = '2.95' ; 2025-06-04 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/05/18, NUV SG Spatial flat and SJI flats from 2025/05/21-22
;version = '2.96' ; 2025-06-30 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/06/15, NUV SG Spatial flat and SJI flats from 2025/06/18
;version = '2.97' ; 2025-07-07 (Wei Liu) - new iris_dark_trend_fix.pro from SAO: progver = 'v2025.July.07' ;--- (Guliano) V38 (All Ports):All Model F parameters for each port refit for middle of the model to improve alignment; "only a temporary fit to be used moving forward for now (no reprocessing needed)"
;version = '2.98' ; 2025-07-24 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/07/13, NUV SG Spatial flat and SJI flats from 2025/07/18 and 07/16-17, respectively.
;version = '2.99' ; 2025-08-20 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/08/09, NUV SG Spatial flat and SJI flats from 2025/08/13-14;
                                ; the next version = '3.00' will mark a significant change in pipeline processing, using new FUV background2 files.
;version = '3.00' ; 2025-08-21 (Ryan Timmons) - v2 of FUV background correction (iris_prep_get_back2) is now used for all time ranges (previous versions were pre 2023 data for testing only)
;version = '3.01' ; 2025-09-19 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2025/09/07, NUV SG Spatial flat and SJI flats from 2025/09/10;
;version = '3.02' ; 2025-10-05 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: new FUV background2 from 2025/09/07.
;version = '3.03' ; 2025-10-17 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: new FUV background2 from 2025/10/04, NUV SG Spatial flat from 2025/10/08,  SJI flats from 2025/10/07;
;version = '3.04' ; 2026-01-03 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: No FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2025/11/05 and 2025/12/04-05
;version = '3.05' ; 2026-01-09 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: No FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2025/12/31-2026/01/01
;version = '3.06' ; 2026-02-12 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: No FUV background b/c eclipse season, NUV SG Spatial flat and SJI flats from 2026/01/28
;version = '3.07' ; 2026-03-25 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: FUV background from 2026/02/21 (1st one after eclipse season),  NUV SG Spatial flat and SJI flats from 2026/02/25-26
;version = '3.08' ; 2026-04-03 (Wei Liu) - marking updates from JPW/Chunming Zhu @MSU: FUV background from 2026/03/21, NUV SG Spatial flat and SJI flats from 2026/03/25
;version = '3.09' ; 2026-05-08 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2026/04/19,  NUV SG Spatial flat and SJI flats from 2026/04/22
 version = '3.10' ; 2026-06-30 (Wei Liu) - marking updates from Chunming Zhu @MSU: FUV background from 2026/05/17 and 2026/06/14,  NUV SG Spatial flat and SJI flats from 2026/05/20-05/21 and 2026/06/17-06/18

if KEYWORD_SET(only_version) then RETURN
if verbose then PRINT, 'Running IRIS_PREP.PRO ', version

; Set up to handle case where only header is to be processed
if KEYWORD_SET(keyword_only) then begin
	nosat = 1
	nobad = 1
	nodark = 1
	noflat = 1
	noback = 1
	pipeline = 0
	nrt_pipeline = 0
	kludge_fuv = 0
endif else keyword_only = 0

; Set batches of keywords if it is being run in the near-real-time pipeline
if KEYWORD_SET(nrt_pipeline) or KEYWORD_SET(_nrt_pipeline) then begin
       poly2d = 1
       update_roll = 1
       measure_aia = 0
       post_warp = 0
       verbose = 1
       run_time = 1
       shift_wave = 1
       shift_fid = 1
       write = 0
       pipeline = 0
endif

; Set batches of keywords if it is being run in the pipeline
if KEYWORD_SET(pipeline) then begin
	poly2d = 1
	update_roll = 1
	verbose = 1
	run_time = 1
	shift_wave = 1
	shift_fid = 1
	filter_fid = 1
	filter_wave = 1
	filter_aia = 1
	dose = 1
	ccdstat = 1
	if KEYWORD_SET(do_filter_faint_fids) then dont_filter_faint_fids = 0 $
		else dont_filter_faint_fids = 1
endif

; Ensure that /shift_X is set if /filter_X is set
if KEYWORD_SET(filter_fid) then shift_fid = 1
if KEYWORD_SET(filter_wave) then shift_wave = 1
if KEYWORD_SET(filter_aia) then shift_aia = 1

; Define paths to ancillary data
if not KEYWORD_SET(logdir) then logdir = '/irisa/data/prep/'

iintype = SIZE(iindex, /tname)
case iintype of
	'STRUCT'	:	begin				; Case of index/data inputs
						input_mode = 'index_data'
						iindex0 = iindex[0]
						n_img = N_ELEMENTS(iindex)
					end
	'STRING'	:	begin				; Case of file list/index list inputs
						input_mode = 'file_list'
						file_list = iindex
						if N_ELEMENTS(idata) eq 0 then $
							ss_infile = INDGEN(N_ELEMENTS(file_list)) $
							else ss_infile = idata
						ss_not_exist = WHERE(FILE_EXIST(file_list[ss_infile]) ne 1, n_not_exist)
						if n_not_exist gt 0 then begin
							BOX_MESSAGE, ['IRIS_PREP: Not all files found.', 'Returning...']
							RETURN
						endif
						n_img = N_ELEMENTS(ss_infile)
						infile_arr = iindex[ss_infile]
						READ_IRIS, infile_arr, iindex, idata, _extra=_extra
					end
	else		:	begin				; Funny input specified
						BOX_MESSAGE, ['IRIS_PREP: Specify either header array', $
							'or list of filenames to read. Returning...']
						RETURN
					end
endcase

; Do some basic checks on the internal consistency of the data
quality = IRIS_PREP_CHECKSIZE(iindex, idata, imgpath = imgpath, $
	sumspat = sumspat, sumsptrl = sumsptrl, datasize = datasize, $
	keyword_only = keyword_only, masks= masks)
if STRMID(imgpath, 0, 3) eq 'SJI' then isspec = 0 else isspec = 1

; Check for mixed image types on input, or a weird image size
if quality mod 64 ne 0 then begin
	errmsg = 'IRIS_PREP encountered a fatal error and is returning:'
	if (quality and 1) ne 0 then errmsg = [errmsg, 'Mixed image paths...']
	if (quality and 2) ne 0 then errmsg = [errmsg, 'Mixed sumspat or NAXIS2...']
	if (quality and 4) ne 0 then errmsg = [errmsg, 'Mixed sumsptrl or NAXIS1...']
	if (quality and 8) ne 0 then errmsg = [errmsg, 'Unexpected image size...']
	if (quality and 16) ne 0 then errmsg = [errmsg, 'Bad T_OBS (corrupt ISP)...']
	if (quality and 32) ne 0 then errmsg = [errmsg, 'Unexpected win_flip...']
	BOX_MESSAGE, errmsg
	if strict then begin
		oindex = iindex
		if (keyword_only eq 0) then odata = !values.f_nan * idata
	endif
	RETURN
endif

; Check for lvl_num keyword
itags = TAG_NAMES(iindex)
lvlnum_tag = WHERE(itags eq 'LVL_NUM', haslvl)
if haslvl then if iindex[0].lvl_num ne 1 then begin
	BOX_MESSAGE, ['IRIS_PREP: Non-lev1 data input', 'I hope you know what youre doing...']
	if strict then begin
		oindex = iindex
		if (keyword_only eq 0) then odata = !values.f_nan * idata
		RETURN
	endif
endif

; Turn off application of fiducial fitter on FUV SJIs if /dont_filter_faint_fids is set
if KEYWORD_SET(filter_fid) and $
   KEYWORD_SET(dont_filter_faint_fids) and $
   (STRMID(imgpath, 0, 5) eq 'SJI_1' ) then begin
    BOX_MESSAGE, ['IRIS_PREP: /dont_filter_faint_fids is set', 'So we wont...']
    filter_fid = 0
endif

if KEYWORD_SET(pstop) then STOP

;++++++++++++++++++++++++++++++++++++++++
; 1. Generate output variables; 		;
; flag missing and saturated pixels 	;
;----------------------------------------
oindex = IRIS_PREP_ADD_HEADER(iindex)
oindex.iprpver = FLOAT(version)
if (keyword_only eq 0) then begin
	odata = FLOAT(idata)
	missvals = WHERE(idata eq -32768, num_miss)
	if num_miss gt 0 then odata[missvals] = !values.f_nan
endif else begin
	odata = FLTARR(1,1,N_ELEMENTS(iindex))
	if not KEYWORD_SET(noversion) then oindex = IRIS_PREP_GET_VERSIONS(oindex)
endelse

dsize = SIZE(odata)

; Weird win_flip not necessarily fatal for SJIs...
if ( (quality and 64) ne 0) then begin
	; Check for special case of full-frame FUV SJIs
	full_sji_crs = [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 405, 408, 413, 419, 422]
	wherefull = WHERE(oindex[0].iicrsid eq full_sji_crs, isfull)
	if (STRMID(imgpath, 0, 5) eq 'SJI_1') and (isfull gt 0) then begin
		if (keyword_only eq 0) then for i = 0, n_img - 1 do $
			odata[*,*,i] = ROTATE(TEMPORARY(odata[*,*,i]), 5)
		oindex.win_flip = 2
		quality = quality - 64
		masks.flip_mask = masks.flip_mask * 0
		masks.anybit = (masks.imgpath_mask + masks.sumspat_mask + $
			masks.sumsptrl_mask + masks.size_mask + masks.badisp_mask) gt 0
		UPDATE_HISTORY, oindex, 'Re-flipped full-frame FUV SJI'
		BOX_MESSAGE, ['IRIS_PREP: Full-frame FUV SJI', 'Re-flipping and carrying on...']
	endif else begin
		BOX_MESSAGE, ['IRIS_PREP: Unexpected win_flip', 'Proceeding with processing...']
	endelse
endif

if not KEYWORD_SET(nosat) then begin
	if N_ELEMENTS(sat_thresh) eq 0 then sat_thresh = 1.6e4
	satpix = WHERE(odata ge sat_thresh, nsatpix)
	if nsatpix gt 0 then begin
		odata[satpix] = !values.f_infinity
		UPDATE_HISTORY, oindex, 'Set ' + STRTRIM(nsatpix,2) + ' saturated pixels to Inf'
	endif
endif

; Look up temperatures for the interval spanning all observations 
; and 1 hour previous, and populate the temperature keywords in the header
tsecs = ANYTIM(oindex.t_obs)
startt = ANYTIM(MIN(tsecs)-4000, /ccsds)
endt = ANYTIM(MAX(tsecs)+1000, /ccsds)
if (not header_temps) and ( (not nodark) or (not nowarp) ) then begin
	; Load and cache temperature defaults
	common IRIS_PREP_DEFAULT_TEMPS, default_temps
	if N_ELEMENTS(default_temps) eq 0 then begin
		sswdata = CONCAT_DIR('$SSW_IRIS','data')
		CD, sswdata, current = old_dir
		RESTGEN, file = 'iris_default_temp.genx', str = default_temps
		CD, old_dir
	endif
	; Load and cache relevant temperatures from housekeeping
	common IRIS_PREP_HK_TEMPS, alltemps
	temps_cached = 0
	if N_ELEMENTS(alltemps) gt 0 then begin
		tcache_tlim = LIMITS(ANYTIM(alltemps.date_obs))
		if (tcache_tlim[0] le (startt + 400)) and (tcache_tlim[1] ge (endt - 900)) then temps_cached = 1
	endif
	if temps_cached eq 0 then alltemps = IRIS_TIME2HK(startt, endt, /temps)
	temptags = N_TAGS(alltemps)
	if temptags eq 0 then begin		
		; If there was no temperature file, just make a flat one
		if KEYWORD_SET(verbose) then PRINT, 'IRIS_PREP: No temperatures found!'
		time_tab = [startt, endt]
		alltemps = REPLICATE(default_temps, 2)
	endif else begin
		time_tab = alltemps.date_obs
	endelse
	temptagnames = TAG_NAMES(alltemps)
	deftagnames = TAG_NAMES(default_temps)
	ttag_list = ['IT15SPPY', 'IT17SPNY', 'IT18SPPZ', 'IT19SPNZ', 'IT01PMRF', 'IT06TELM']
	; If update_roll is set, then also update the temperature keywords in the header
	if KEYWORD_SET(update_roll) then ttag_list = [ttag_list, 'ITF1CCD1', 'ITF2CCD2', $
		'ITNUCCD3', 'ITSJCCD4', 'BT06CBPX', 'BT07CBNX', 'BT15IEB', 'IT08GTWM', 'IT14SPPX', 'IT16SPNX']
	for i = 0, n_img -1 do begin
		for j = 0, N_ELEMENTS(ttag_list) - 1 do begin
			ttag_index = WHERE(temptagnames eq ttag_list[j])
			hdr_t_index = WHERE(TAG_NAMES(oindex) eq ttag_list[j])
			temp_tab = alltemps.(ttag_index)
			missing_temps = WHERE(temp_tab lt -9998., nmt)
			case 1 of
				nmt eq N_ELEMENTS(temp_tab)	: fixval = default_temps.(WHERE(deftagnames eq ttag_list[j]))
				nmt eq 0					: fixval = -9999
				else						: fixval = MEAN(temp_tab[WHERE(temp_tab ge -9998.)])
			endcase
			if nmt gt 0 then temp_tab[missing_temps] = fixval
			oindex[i].(hdr_t_index) = INTERPOL(temp_tab, ANYTIM(time_tab), ANYTIM(oindex[i].t_obs))		
		endfor
	endfor
	numtime = N_ELEMENTS(time_tab)
endif

; Look up roll and orbital phase for the interval spanning all observations and
; update the headers
if KEYWORD_SET(update_roll) then begin
	common IRIS_PREP_HK_POINT, newpoint
	point_cached = 0
	if N_ELEMENTS(newpoint) gt 0 then begin
		pcache_tlim = LIMITS(ANYTIM(newpoint.date_obs))
		if (pcache_tlim[0] le (startt + 400)) and (pcache_tlim[1] ge (endt - 900)) then point_cached = 1
	endif
	if point_cached eq 0 then newpoint = IRIS_TIME2HK(startt, endt, /magnetometer)
	pointtags = N_TAGS(newpoint)
	if pointtags eq 0 then begin		
		; If you couldn't find the roll/phase online, just leave them alone
		if KEYWORD_SET(verbose) then PRINT, 'IRIS_PREP: Unable to update roll/phase'
	endif else begin
		point_time_tab = newpoint.date_obs
		for i = 0, n_img -1 do begin
			oindex[i].ophase = INTERPOL(newpoint.ophase, ANYTIM(point_time_tab), ANYTIM(oindex[i].t_obs))
			oindex[i].sat_rot = INTERPOL(newpoint.a_eulerbr_z, ANYTIM(point_time_tab), ANYTIM(oindex[i].t_obs))
		endfor
	endelse
endif

;+++++++++++++++++++++++++++++++++++
; 2. Apply dark/flatfield correction
;
;-----------------------------------

; Update a running library of text files giving statistics on the CCD overscan/BLS/etc.
if KEYWORD_SET(ccdstat) then IRIS_PREP_CCDSTAT_LOGGER, oindex, odata, logdir = logdir

; Apply dark and note it in the header
if not nodark then begin
	dmsgs = STRARR(n_img)
	if header_temps then for i = 0, n_img - 1 do begin	
	;	Just rely on whatever iris_make_dark does with what's in the headers
		odata[*,*,i] = IRIS_PREP_DARK(TEMPORARY(odata[*,*,i]), oindex[i], dmsg = dmsg)
		dmsgs[i] = dmsg
	endfor else begin
	; 	Use the previously-looked-up temperature values
		temp_tab = FLTARR(6, numtime)
		temp_tab[0,*] = alltemps.ITF1CCD1
		temp_tab[1,*] = alltemps.ITF2CCD2
		temp_tab[2,*] = alltemps.ITNUCCD3
		temp_tab[3,*] = alltemps.ITSJCCD4
		temp_tab[4,*] = alltemps.BT06CBPX
		temp_tab[5,*] = alltemps.BT07CBNX
		if KEYWORD_SET(pstop) then STOP
		for i = 0, n_img - 1 do begin	
			odata[*,*,i] = IRIS_PREP_DARK(TEMPORARY(odata[*,*,i]), oindex[i], $
				time_tab = time_tab, temp_tab = temp_tab, dmsg = dmsg, $
				tempstring = tempstring, dversion = dversion)
			oindex[i].iprpdtmp = tempstring
			oindex[i].iprpdver = dversion
			dmsgs[i] = dmsg
		endfor		
	endelse
	UPDATE_HISTORY, oindex, dmsgs, /mode
endif

; Subtract out the FUV background
if not KEYWORD_SET(noback) and imgpath eq 'FUV' then begin
                                ;RPT 8/21/2025 new background mode is
                                ;the default for all, removed time-threshold check
        ;tsecs = ANYTIM(oindex.t_obs)
        ;tsecsthresh = ANYTIM('2023-01-01 00:00:00')
     
        ;if (tsecs[0] lt tsecsthresh) then begin
          ; print, 'using new 2024 background method'
            for i = 0, n_img - 1 do begin
               thisback = IRIS_PREP_GET_BACK2(oindex[i], fbver, history=bghist)
               if N_ELEMENTS(thisback) gt 1 then odata[*,*,i] = odata[*,*,i] - thisback
            endfor
            oindex.iprpbver = fbver[0]
            ;print, 'got full bghist:'
            ;print, bghist
            UPDATE_HISTORY, oindex, bghist
        ;endif else begin        ; old background method
        ;   print, 'using original background'
        ;   for i = 0, n_img - 1 do begin
        ;      thisback = IRIS_PREP_GET_BACK(oindex[i], fbver)
        ;      if N_ELEMENTS(thisback) gt 1 then odata[*,*,i] = odata[*,*,i] - thisback
        ;   endfor
        ;   oindex.iprpbver = fbver[0]
        ;   UPDATE_HISTORY, oindex, 'FUV background subtracted'
        ;endelse
        
endif

; Apply a kludgy fix for the FUV pedestal variation
if KEYWORD_SET(kludge_fuv) and imgpath eq 'FUV' then begin
	submeds = FLTARR(2,2)
	for i = 0, 1 do for j = 0, 1 do begin
		xoff = i*dsize[1]/2
		xrange = dsize[1]/2-1
		yoff = j*dsize[2]/2
		yrange = dsize[2]/2-1
		subimg = odata[xoff:xoff+xrange,yoff:yoff+yrange,*]
		submeds[i,j] = MEDIAN(subimg[WHERE(subimg lt MEDIAN(subimg))]) - 0.5
		odata[xoff:xoff+xrange,yoff:yoff+yrange,*] = subimg - submeds[i,j]
	endfor
	UPDATE_HISTORY, oindex, 'Kludged dark: ' + STRING(REFORM(submeds,4), form = '(4f8.2)')
endif

; Update a running library of FITS files indicating how many photons have hit each pixel
if KEYWORD_SET(dose) then IRIS_PREP_DOSE_LOGGER, oindex, odata, logdir = logdir

; Apply flatfield and note it in the header
if not KEYWORD_SET(noflat) then begin
	fmsgs = STRARR(n_img)
	for i = 0, n_img - 1 do begin
		odata[*,*,i] = IRIS_PREP_FLAT(TEMPORARY(odata[*,*,i]), oindex[i], $
			frecnum = frecnum, fmsg = fmsg, nospat = nospat)
		oindex[i].iprpfver = frecnum
		fmsgs[i] = fmsg
	endfor
	UPDATE_HISTORY, oindex, fmsgs, /mode 
endif

if KEYWORD_SET(pstop) then STOP
if run_time and verbose then $
	PRINT, 'IRIS_PREP: Flat/dark...', SYSTIME(/sec) - t0, form = '(a30,f10.2)'

;+++++++++++++++++++++++++++++++++++
; 3. Set permanently bad pixels to
; zero 
;-----------------------------------
if not KEYWORD_SET(nobad) then begin
	if imgpath eq 'FUV' then fsize = 4144l else fsize = 2072l
	badpix = IRIS_PREP_GET_BADPIX(oindex[0], badpix_recnum = badpix_recnum)
	bpx = badpix mod fsize
	bpy = badpix / fsize
	bpmask = FLTARR(dsize[1], dsize[2]) + 1.
	bpmask[bpx/sumsptrl, bpy/sumspat]  = 0.
	for i = 0, n_img - 1 do begin
		odata[*,*,i] = odata[*,*,i] * bpmask
	endfor
	oindex.iprppver = badpix_recnum
	UPDATE_HISTORY, oindex, 'Set permanently bad pixels to 0 prior to warping'
endif

;+++++++++++++++++++++++++++++++++++
; 4. Despike (optional, and not
; generally recommended)
;-----------------------------------
case 1 of

	;	Run iris_prep_despike in real time if despike_here is set...
	KEYWORD_SET(despike_here)	:	begin
		if N_ELEMENTS(spikefile) gt 0 then begin
			MESSAGE, 'Keyword /despike_here means that spikefile will be ignored...'
		endif
		for i = 0, n_img - 1 do begin
			odata[*,*,i] = IRIS_PREP_DESPIKE(TEMPORARY(odata[*,*,i]))
;			dummy = IRIS_PREP_DESPIKE(TEMPORARY(odata[*,*,i]), goodmap = goodmap)
;			tt = oindex[i].t_obs			
;			this_spikefile = '~/Desktop/scratch/ispike/iris_' + TIME2FILE(tt, /sec) + $
;				STRMID(tt,20,2) + '_' + STRLOWCASE(STRMID(oindex[i].img_path, 0, 3)) + $
;				'_spikes.fits'
;			WRITEFITS, this_spikefile, goodmap
		endfor
		UPDATE_HISTORY, oindex, 'ran IRIS_PREP_DESPIKE'
		if run_time and verbose then $
			PRINT, 'IRIS_PREP: Despiked...', SYSTIME(/sec) - t0, form = '(a30,f10.2)'
	end

	;	Use a previously-run set of spikes if spikefile is set
	N_ELEMENTS(spikefile) gt 0 	:	begin
		; If set as a switch, find spikefiles for all images
		if spikefile[0] eq '1' then spikefile = STRARR(n_img)
		; Repair the spikes in the spikefile
		for i = 0, n_img - 1 do begin
			if spikefile[i] eq '' then begin
				tt = oindex[i].t_obs
				this_spikefile = '/irisa/data/spike_del/aia/lev1/' + $
					STRMID(tt, 0, 4) + '/' + STRMID(tt, 5, 2) + '/' + STRMID(tt, 8,2) + $
					'/H' + STRMID(tt,11,2) + '00/iris' + TIME2FILE(tt, /sec) + $
					STRMID(tt,20,2) + '_' + STRLOWCASE(STRMID(oindex[i].img_path, 0, 3)) + $
					'spikes.fits'
				if FILE_EXIST(this_spikefile) then spikefile[i] = this_spikefile
			endif
			if spikefile[i] ne '' then begin
				READ_IRIS, spikefile[i], spikehead, spikedat
				tmpdata = odata[*,*,i]
				tmpdata[spikedat[*,0]] = spikedat[*,2]
				odata[*,*,i] = tmpdata
			endif
		endfor
		UPDATE_HISTORY, oindex, 'used spikefile to replace spikes'
		if run_time and verbose then $
			PRINT, 'IRIS_PREP: Despiked...', SYSTIME(/sec) - t0, form = '(a30,f10.2)'
	end
	
	; Generally, don't worry about the spikes
	else	:

endcase

;+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
; 5. Warp the image
;	- Look up interpolation matrix used to straighten spectral lines (identity matrix for SJI)
;	- Apply scaling, rotation and shift specified for each image type by pointing database
;	- Optionally, apply additional time-varying shifts based on measurements of fiducials/neutral lines
;	- Update the headers to reflect the shifts/warping
;	- Optionally, update the headers to reflect correlation with SDO images
;-------------------------------------------------------------------------------------------------------
if not nowarp then begin

	; Select the algorithm and parameters that will be used for warping
	if not KEYWORD_SET(cubic) then cubic = -0.5
	SETENV, 'IRIS_PREP_POLY2D='+STRTRIM(poly2d,2)

	; Determine how the CRS boxes should be affected by the warping based on
	; the minbox/maxbox keywords
	case 1 of
		KEYWORD_SET(maxbox)	:	boxwarp = 1
		KEYWORD_SET(minbox)	:	boxwarp = 0
		KEYWORD_SET(samebox):	boxwarp = 2
		else				:	boxwarp = 1
	endcase

	; Look up geometric/wavelength calibration parameters
	geowave_params = IRIS_PREP_GET_GEOWAVE(oindex[0])
	if imgpath eq 'FUV' then geover = geowave_params.fuvs.rec_num $
		else geover = geowave_params.rec_num	
	pdb = IRIS_MK_POINTDB(version = pdb_ver)
	
	; Decide whether to write the alignment results to txt files
	if KEYWORD_SET(write) then begin
		al_logdir = logdir
		if KEYWORD_SET(post_warp) then nowarp_logdir = 0 else nowarp_logdir = logdir
	endif else begin
		al_logdir = 0
		nowarp_logdir = 0
	endelse
	
	; Shift the image to put the fiducials where they're supposed to be based on
	; long-term temperature trends
	if KEYWORD_SET(shift_fid) then fidmsgs = STRARR(n_img) else shift_fid = 0
	
	; Shift the image to put the reference wavelength exactly where it's supposed to be
	if KEYWORD_SET(shift_wave) and (isspec eq 1) then begin
		do_shift_wave = 1
		wavemsgs = STRARR(n_img)
	endif else begin
		do_shift_wave = 0
	endelse

	; Update the headers to identify the shifts needed to coalign with SDO
	if KEYWORD_SET(shift_aia) then aiamsgs = STRARR(n_img) else shift_aia = 0
	
	; If you're running on dummy data, then ignore the /filter_* and /measure_* keywords
	if N_ELEMENTS(idata) lt 2 then begin
		do_measure_wave	= 0
		do_measure_fid	= 0
		do_measure_aia	= 0
		do_filter_wave	= 0
		do_filter_fid	= 0
		do_filter_aia	= 0
		obsfit = ''
		do_post = 0
		xfitflag = 0
	endif else begin
		; Look up the per-OBS fit results on the fiducials, wavelength correction, 
		; and AIA cross-correlation so that they can be applied
		if KEYWORD_SET(filter_fid) then do_filter_fid = 1 else do_filter_fid = 0
		if KEYWORD_SET(filter_wave) then do_filter_wave = 1 else do_filter_wave = 0
		if KEYWORD_SET(filter_aia) then do_filter_aia = 1 else do_filter_aia = 0
		if KEYWORD_SET(filter_fid) or KEYWORD_SET(filter_wave) or KEYWORD_SET(filter_aia) then begin
			if KEYWORD_SET(obsfile) gt 0 then begin
				RESTGEN, file = obsfile, str = obsfit
			endif else begin
				obsfit = IRIS_PREP_OBSFIT_READER(oindex)
			endelse
			if N_TAGS(obsfit) eq 0 then begin
				BOX_MESSAGE, ['IRIS_PREP: Missing obsfit.genx', oindex[0].t_obs]
				do_filter_fid = 0
				do_filter_wave = 0
				do_filter_aia = 0
			endif
		endif else begin
			obsfit = ''
		endelse
		if KEYWORD_SET(measure_fid) then do_measure_fid = 1 else do_measure_fid = 0
		if KEYWORD_SET(measure_wave) then do_measure_wave = 1 else do_measure_wave = 0
		if KEYWORD_SET(post_warp) then begin
			do_post = 1
			if do_measure_fid + do_measure_wave gt 0 then $
				BOX_MESSAGE, ['IRIS_PREP: /measure_fid and /measure_wave are not needed', $
					'if /post_warp is set, and their results are discarded.', $
					'But we will leave them set and assume you know what you are doing...']
		endif else begin
			do_post = 0
		endelse
		if do_shift_wave or (shift_fid and (isspec eq 0) ) then xshiftflag = 1 else xshiftflag = 0
		if do_filter_wave or (do_filter_fid and (isspec eq 0) ) then xfitflag = 1 else xfitflag = 0
		oindex[*].iprpofff = xshiftflag + (2 * xfitflag) + (16 * shift_fid) + (32 * do_filter_fid)
		; The AIA correlation requires an environmental rather than a local variable
		if KEYWORD_SET(measure_aia) then begin
			aia_logdir = CONCAT_DIR(al_logdir, 'aiacorr')
			do_measure_aia = 1
		endif else begin
			do_measure_aia = 0
		endelse
	endelse

	; For FUV, need separate S/L messages for the wavelength and fiducial finder 
	if imgpath eq 'FUV' then begin
		if N_ELEMENTS(wavemsgs) ne 0 then lwavemsgs = wavemsgs
		if N_ELEMENTS(fidmsgs) ne 0 then lfidmsgs = fidmsgs
	endif
	
	; Apply geometric/wavelength calibration, along with thermal drift fixes
	for i = 0, n_img - 1 do begin
		; Modify the warping parameters to do shifting, rotation, scaling
		this_geowave_params = IRIS_PREP_ALIGN_IMAGE(oindex[i], odata[*,*,i], $
			geowave_params, pdb, fidmsg = fidmsg, wmsg = wmsg, logdir = nowarp_logdir, $
			measure_fid = do_measure_fid, shift_fid = shift_fid, obsfit = obsfit, loud = loud, $
			filter_fid = do_filter_fid, filter_wave = do_filter_wave, $
			measure_wave = do_measure_wave, shift_wave = do_shift_wave, pstop = (pstop gt 1), $
			xfiltfail = xfiltfail, yfiltfail = yfiltfail, fitchisq_max = fitchisq_max)
		; Apply the warping/shifting/rotation/scaling to the image and header
		odata[*,*,i] = IRIS_PREP_GEOWAVE_CORRECT(/update, TEMPORARY(odata[*,*,i]), $
			this_geowave_params, inhead=oindex[i], outhead = nindex, $
			/boxwarp, cubic = cubic, keyword_only = keyword_only, pstop = (pstop gt 1), check = check)
		; If requested, do the fiducial and wavelength measurements after warping
		; These measurements are not reported in the header or folded back into the image
		if do_post then begin
			nindexi = nindex
			if haslvl then nindexi.lvl_num = 1.5 else nindexi = ADD_TAG(nindexi, 1.5, 'LVL_NUM')
                	dummy = IRIS_PREP_ALIGN_IMAGE(nindexi, odata[*,*,i], $
				this_geowave_params, pdb, logdir = al_logdir, /measure_fid, /measure_wave, $
				pstop = (pstop gt 1), /level1p5, loud = loud)
		endif
		; Measure and/or apply shift to header WCS to align with SDO 
                if do_measure_aia and (imgpath eq 'SJI_1330' or imgpath eq 'SJI_1400' or imgpath eq 'SJI_2832') $
                    then begin
			iris_align_str = IRIS_AIA_CORR( nindex, odata[*,*,i], do_log=KEYWORD_SET(write), $
				/quiet, /short, use_lev1p5=0, pstop=pstop, logdir = aia_logdir)
			if shift_aia then nindex = IRIS_ALIGN_AIA(nindex, iris_align_str, msg = aiamsg)
		endif else if do_filter_aia then nindex = IRIS_ALIGN_AIA(nindex, obsfit, msg = aiamsg) $
                                            else aiamsg=''

		; Document shifts applied
		if do_shift_wave then begin
			wavemsgs[i] = wmsg[0]
			nindex.iprpoffx = FLOAT(STRMID(wmsg[0], 40, 9))
		endif
		if shift_fid then begin
			fidmsgs[i] = fidmsg[0]
			if (isspec eq 1) then begin
				nindex.iprpoffy = FLOAT(STRMID(fidmsg[0], 40, 9))
			endif else begin
				nindex.iprpoffx = FLOAT(STRMID(fidmsg[0], 40, 9))
				nindex.iprpoffy = FLOAT(STRMID(fidmsg[0], 49, 9))
			endelse
		endif
		if (xfitflag eq 1) and (xfiltfail eq 1) then nindex.iprpofff = nindex.iprpofff + 4
		if (do_filter_fid eq 1) and (yfiltfail eq 1) then nindex.iprpofff = nindex.iprpofff + 64
		if shift_aia then aiamsgs[i] = aiamsg[0]
		if imgpath eq 'FUV' then begin
			if do_shift_wave then lwavemsgs[i] = wmsg[1]
			if shift_fid then lfidmsgs[i] = fidmsg[1]
		endif
		
		; Set up the array of the warped headers to replace the old headers
		if i eq 0 then begin
			newindex = nindex
			indtemplate = nindex
		endif else begin
			STRUCT_ASSIGN, nindex, indtemplate
			newindex = [newindex, indtemplate]
		endelse

	endfor
	oindex = newindex
	oindex.iprppdbv = pdb_ver
	oindex.iprpgver = geover
	UPDATE_HISTORY, oindex, 'Used iris_mk_pointdb ver ' + STRTRIM(pdb_ver, 2)
	if do_shift_wave then UPDATE_HISTORY, oindex, wavemsgs, /mode
	if shift_fid then UPDATE_HISTORY, oindex, fidmsgs, /mode
	if shift_aia then UPDATE_HISTORY, oindex, aiamsgs, /mode
	if imgpath eq 'FUV' then begin
		if do_shift_wave then UPDATE_HISTORY, oindex, lwavemsgs, /mode
		if shift_fid then UPDATE_HISTORY, oindex, lfidmsgs, /mode
	endif
	if poly2d eq 1 then begin
		UPDATE_HISTORY, oindex, 'Used INF_POLY_2D for warping'
	endif else begin
		UPDATE_HISTORY, oindex, 'Used INFTERPOLATE for warping'
	endelse
	
	if KEYWORD_SET(pstop) then STOP
	if run_time and verbose then $
		PRINT, 'IRIS_PREP: Warping...', SYSTIME(/sec) - t0, form = '(a30,f10.2)'

endif

;+++++++++++++++++++++++++++++++++++
; 6. Convert to physical units
; (and replace missing pixels with
; dummy values if requested)
;-----------------------------------
if KEYWORD_SET(photons) then begin
	odata = IRIS_PREP_CONVERT2PHOTONS(TEMPORARY(odata), inhead = oindex, outhead = nindex)
	oindex = nindex
endif

; If the missing keyword is set to something, then poke that value into all the
; pixels marked as missing (with NaNs)
if N_ELEMENTS(missing) ne 0 then begin
	missind = WHERE(odata ne odata, nummiss)
	if nummiss ne 0 then odata[missind] = missing
endif

; If the desat keyword is set to something, then poke that value into all the
; pixels marked as saturated (with Infs)
if N_ELEMENTS(desat) ne 0 then begin
	if desat eq 1 then desat = 16384.
	desat = desat[0]
	satind = WHERE(odata eq !values.f_infinity, nsatpix_1p5)
	if nsatpix_1p5 ne 0 then odata[satind] = desat
endif

if KEYWORD_SET(scaled) then IRIS_PREP_FLOAT2INT, ohdr, TEMPORARY(odata), ohdr, odata

;+++++++++++++++++++++++++++++++++++
; 7. Update FITS header 
;-----------------------------------
if haslvl then oindex[*].lvl_num = 1.5 else oindex = ADD_TAG(oindex, 1.5, 'LVL_NUM')
if (keyword_only eq 0) then oindex = IRIS_PREP_IMAGE_STATS(oindex, odata)
UPDATE_HISTORY, oindex, caller = 'iris_prep', version = version
UPDATE_HISTORY, oindex, ' ran on ' + TIME2FILE(/sec, RELTIME(/now))
oindex.keywddoc = 'http://www.lmsal.com/iris_science/irisfitskeywords.pdf'
oindex.iprpver	= version

;+++++++++++++++++++++++++++++++++++
; 8. Clean up and exit
;-----------------------------------
if input_mode eq 'file_list' then begin
	; put the input variables back
	iindex = file_list
	idata = ss_infile
endif
if KEYWORD_SET(run_time) then begin
	tdelt = SYSTIME(/sec)-t0
	BOX_MESSAGE, $
		[STRING('IRIS_PREP: ', n_img, 'images prepped', format = '(a12, i5, a15)'), $
		 STRING('Run time: ' , tdelt, 'seconds', form = '(a12, f7.1, a8)')]
endif

end