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Last modified: Thu Oct 27 17:25:44 2005.
NAME:
hires_1dspec
Version 1.1
PURPOSE:
Combines orders of a echfspec structure into a 1d spectrum.
Outputs flux and error arrays into separate files (_F.fits, _E.fits)
CALLING SEQUENCE:
hires_1dspec, hires, setup, obj_id, chip
INPUTS:
hires - MIKE structure
obj_id - Object ID (e.g. 0L, 1L, etc)
[exp_id] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
1d flux - (fits file; FSpec/name_ech_F.fits)
1d error - (fits file; FSpec/name_ech_E.fits)
OPTIONAL KEYWORDS:
/SILENT - No text output
OBJ_NM= - Name of object in slit (a = science)
/STD - Run on a standard star
OUTNM= - Alternative output name for FSpec file
ENDTRM= - Trim order edges by this when calculating ratios
MINPIX1= - Minimum 'good' pixels to calculate fitting profile
ORDNM= - 0th or 1st order fitting (1 = 1st, 2 = 0th (default))
SNRMIN= - Minimum S/N per pixel for consideration in fitting
MINPIX2= - Minimum 'good' pixels to calculate simple 0th order fit
OPTIONAL OUTPUTS:
COMMENTS: ;
EXAMPLES:
hires_1dspec, hires, setup, obj_id, chip
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
14-Jun-2004 Written by GEP
(See pro/Spec/hires_1dspec.pro)
NAME:
hires_allarc
Version 1.1
PURPOSE:
Runs through all of the Arc processing steps in one go.
Can be used to process a set of arcs for a given object or all
of the arcs from a given night.
This file also contains hires_allarc_sngl which can be used to
fully process a single arc image. In fact, if the keyword /ALL is
used, then hires_allarc simply loops through all of the arcs calling
hires_allarc_sngl for each one.
CALLING SEQUENCE:
hires_allarc, hires, setup, [chip], /CHK, /CLOBBER, /INDX
INPUTS:
hires - MIKE structure
setup - Integer defining setup OR an array of index values to
process
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
A series of files related to Arc calibration
OPTIONAL KEYWORDS:
/CLOBBER - Overwite any previous files
/CHK - Present GUIs to show results of fitting, etc.
/PINTER - Perform fit for pre-identified lines
/INDX - Treat setup as an array of index values to process
OPTIONAL OUTPUTS:
FITS= - File to write hires structure to (default: 'strct.fits')
ADDITIONAL KEYWORDS TO MIKE_ALLARC_SNGL:
/NOIMG - Do not create arc image
/NOWAV - Do not fit the arc lines (ie. only do tracing)
COMMENTS:
EXAMPLES:
hires_allarc, hires, 1L, 1L, /CHK, /CLOBBER
hires_allarc, hires, [104L, 107L], /INDX
rslt = hires_allarc_sngl('Raw/mb0539.fits', 1, 1, /PINTER)
PROCEDURES/FUNCTIONS CALLED:
hires_fitarc
hires_fit2darc
hires_tracearc
hires_fittrcarc
hires_mkaimg
REVISION HISTORY:
15-Aug-2003 Written by JXP
Usage:
(See pro/Arcs/hires_allarc.pro)
NAME:
hires_allflat
Version 1.1
PURPOSE:
Identifies flats, processes them. Creates one flat file
per slit width. Takes TFLAT as the default
CALLING SEQUENCE:
hires_allaflat, hires, setup
INPUTS:
hires - HIRES structure
setup - Setups (can be an array of values)
[chip] - Chip to process
RETURNS:
OUTPUTS:
One normalized flat per slit width
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_allflat, hires, [1L,2L,3L,4L]
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
Feb-2005 Written by JXP
(See pro/Flat/hires_allflat.pro)
NAME: hires_allobj
Version 1.1
PURPOSE:
Run all of the processing steps on a single object. This
includes processing, CR rejection, tracing, sky subtraction and
extraction. Future version will allow multiple (or all objects)
and also fluxing.
CALLING SEQUENCE:
hires_allobj, hires, setup, obj_id, chip, [exp], /PROCALL
INPUTS:
hires - MIKE structure
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
chip - Blue (1) or Green (2) and/or Red (3) side
[exp] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
/ALLPROC - Perform all steps
/SKYCHK - Check Final sky image
/RESCHK - Check Final extracted image
/DOPROC - Do image processing
/DOFNT - Do object tracing
/DOSKY - Do sky sub
/DOBOX - Do extraction
/NOCR - Turn off CR rejection routine (hires_objcr)
/CLOBBER - Overwrite previous images (mainly the processed image)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_allobj, hires, 1L, 1L
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
26-Apr-2004 Written by JXP
(See pro/Object/hires_allobj.pro)
NAME:
hires_ar
Version 1.1
PURPOSE:
Reads in the first fits file in the directory with name
'hires_*.fits' and passes back the hires structure.
CALLING SEQUENCE:
hires = hires_ar(file)
INPUTS:
[file] - Filename (default: first file in list ./hires_*fits*)
RETURNS:
hires - MIKE structure
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires = hires_ar()
PROCEDURES/FUNCTIONS CALLED:
hires_rslvall
REVISION HISTORY:
13-Nov-2001 Written by JXP
03-Feb-2003 Polished (JXP)
(See pro/General/hires_ar.pro)
NAME:
hires_arctempl
Version 1.1
PURPOSE:
CALLING SEQUENCE:
hires_arctempl, hires, setup, obj_id, [chip], /INTER, LINLIST=, /CHK, /CLOBBER,
SIGREJ=, /DEBUG, IORDR=, /PINTER
INPUTS:
hires - MIKE structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
IDL fit file (one per order) (e.g. Arcs/ArcECH_##fit.idl)
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_arctempl, hires, 1, 1
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
20-Feb-2005 Created by JXP (based on mike_fitarc)
(See pro/Arcs/hires_arctempl.pro)
NAME:
hires_chkcalib
Version 1.1
PURPOSE:
Checks to see what calibrations files are taken or missing
CALLING SEQUENCE:
hires_chkcalib
INPUTS:
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_chkcalib
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
27-Oct-2005 Written by JXP
(See pro/General/hires_chkcalib.pro)
NAME:
hires_chkflux
Version 1.1
PURPOSE:
Fluxes the spectrum using a standard star calibration. Default
is to use the one in CALIBS which is probably good enough for
relative fluxing. Definitely not good enough for absolute.
CALLING SEQUENCE:
hires_flux, hires, setup, obj_id, chip, FLUXFIL=, /CLOBBER, /STD
INPUTS:
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
chip - Blue (1) Green (2) or Red (3)
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
FLUXFIL - File name of standard star for fluxing (default:
$MIKE_DIR/pro/Std/Archive/sens_blue#.fits)
/STD - Extraction should be set for a standard star
/BOXCAR - Flux data from a Boxcar extraction
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_chkflux, hires, setup, obj_id, chip, /CLOBBER
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
02-Sep-2005 JXP
(See pro/Flux/hires_chkflux.pro)
NAME:
hires_combspec
Version 1.1
PURPOSE:
Combines multiple exposures of the same obj
Must be run even on an object with a single exposure
CALLING SEQUENCE:
hires_combspec, hires, setup, obj_id, chip, exp_id
INPUTS:
hires - MIKE structure
obj_id - Object ID (e.g. 0L, 1L, etc)
[exp_id] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
echfspec - ESI fspec structure (fits file; FSpec/name_ech.fits)
OPTIONAL KEYWORDS:
/SILENT - No text output
LIST= - Use an input list to combine (required for multiple
night obs). Output is in 'FSpec/tmp_ech.fits', unless OUTFIL flag set to something.
OBJ_NM= - Name of object in slit (a = science)
/STD - Run on a standard star
OUTNM= - Alternative output name for FSpec file
/NOFLUX - Fill echfspec structure with fx, rather than flux array
ENDTRM= - Trim order edges by this when calculating ratios
MINPIX1= - Minimum 'good' pixels to calculate fitting profile
ORDNM= - Fitting profile order (default: 1)
SNRMIN= - Minimum S/N per pixel for consideration in fitting
OPTIONAL OUTPUTS:
COMMENTS: ;
EXAMPLES:
hires_combspec, hires, setup, obj_id, side
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
04-Jan-2004 Written by JXP
10-Jun-2004 Revisited by GEP
Sep-2005 Revisited by JXP
(See pro/Spec/hires_combspec.pro)
NAME:
hires_conti2d
Version 1.1
PURPOSE:
Reads in the first fits file in the directory with name
'hires_*.fits' and passes back the hires structure.
CALLING SEQUENCE:
hires = hires_ar(file)
INPUTS:
[file] - Filename (default: first file in list ./hires_*fits*)
RETURNS:
hires - MIKE structure
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires = hires_ar()
PROCEDURES/FUNCTIONS CALLED:
hires_rslvall
REVISION HISTORY:
13-Nov-2001 Written by JXP
03-Feb-2003 Polished (JXP)
(See pro/Spec/hires_conti2d.pro)
NAME:
hires_delov
Version 1.0
PURPOSE:
Deletes OV images
CALLING SEQUENCE:
hires_delov, hires, indx
INPUTS:
hires - ESI structure
indx - Index numbers of frames to delete
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_delov, hires, indx
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
18-Jul-2002 Written by JXP
(See pro/General/hires_delov.pro)
NAME:
hires_edgeflat
Version 1.1
PURPOSE:
This is mainly a frontend to x_edgeflat. See that routine for
extensive (and the most recent) details
CALLING SEQUENCE:
hires_edgeflat, hires, setup, [side], /CHK,
INPUTS:
hires - MIKE structure
setup - Setup identifier
[side] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
A structure containing the information for the order by order
fits. This structure is then fed to hires_fittflat to create a 2D
solution. Typical name: 'Flats/TStr_B_01.fits'
OPTIONAL KEYWORDS:
/CHK -- Check the order edges interactively (similar to INTER)
/INTER -- Determine the order edges interactively
SMSHROW -- Row where order edges are determined (default: 1/2 way
up the image)
THRESH -- Threshold for an order edge on the red side
(default: 100.)
/CLOBBER -- Overwrite the output structure
P_NSIG -- Number of sigma significance that an order edge should
have for the red side (default: 50.)
NSIG -- Number of sigma significance that an order edge should
have fo the blue side (default: 2.0)
MINFLAT -- Mininum counts in flat on blue side to use orders (100)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_edgeflat, hires, 1.0
PROCEDURES/FUNCTIONS CALLED:
hires_edgeflat_clean
hires_getfil
x_edgeflat
REVISION HISTORY:
Feb-2005 Written by JXP
(See pro/Flat/hires_edgeflat.pro)
NAME:
hires_editstrct
Version 1.1
PURPOSE:
Launches a gui to edit the MIKE structure
CALLING SEQUENCE:
hires_editstrct, hires
INPUTS:
hires -- ESI structure
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_editstrct, hires
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
04-Jan-2002 Written by JXP
29-Jan-2003 Polished by JXP
(See pro/General/hires_editstrct.pro)
NAME:
hires_extract
Version 1.1
PURPOSE:
Extract 1D spectra from the 2D images. For each order, a boxcar
and an optimal extraction is performed. For the latter, an object
profile is derived and both the object flux and sky are fit throughout
the order (i.e. not row by row). The main driver is
mike_box_sngl. For the optimal extraction, the data is extracted
to a specific set of vacuum wavelengths, chosen to be the same for
every spectrum to facilitate coadding without rebinning. Here are
the steps in detail:
1. Perform a boxcar extraction using extract_box
2. Estimate the SNR per order from the boxcar extraction
-- LOOP ON ORDERS IN DECREASING SNR --
3. Fit the boxcar extraction with a bspline
4. Calculate the object profile
a. bspline_iterfit the flux vs position on slit
b. Force the profile to be positive everywhere and have a
sensible FWHM
5. Fit the order using the profile and sky (bspline_extract)
CALLING SEQUENCE:
hires_extract, hires, setup, obj_id, chip, [exp], /RESCHK, /CHK
INPUTS:
hires - MIKE structure
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
chip - Blue (1), Green (2) OR Red (3) chip
[exp] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
Fills up the 1D spectral tags in the Object structure.
OPTIONAL KEYWORDS:
/OCHK - Plot the extracted flux (optimal) for each order
/RESCHK - Check the residuals of the 2D, fully extracted image
/STD - Extraction should be set for a standard star
/DEBUG - Stop within extraction routine to check stuff
/SKIPSKYSUB - Perform extraction on the processed but NOT sky
subtracted image.
HIGHSNR - Value of SNR^2 of the data for a given order which when
exceeded mike_box uses an additional parameter for the
profile shape. (Default: 500 corresponding to SNR=22)
Lowering this parameter may improve extraction.
ORDRS - Input array of physical order numbers to extract
/SCTCHK - Show the scattered light image
Optional OUTPUTS:
COMMENTS:
The program extracts the orders in order of decreasing SNR. If the
SNR is lower than lowsnr (default: 2.49) then the optimal
extraction is performed using the profile parameters from the
previous order(s).
EXAMPLES:
hires_extract, hires, 1L, [0L]
PROCEDURES/FUNCTIONS CALLED:
x_echextobj
extract_boxcar
smooth_mask
bspline_extract
REVISION HISTORY:
26-Aug-2003 Written by SMB
(See pro/Object/hires_extract.pro)
NAME:
hires_findgain
Version 1.1
PURPOSE:
Calculate the inverse gain using the routine hires_gain and the Milky Flats.
The value of the gain is then saved into hires.gain
CALLING SEQUENCE:
hires_findgain, hires, setup, [side]
INPUTS:
setup - Setup ID
[side] - Blue (1) and/or Red (2) side [default: [1,2] ]
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
26-Jun-2004 Written by SMB
(See pro/Flat/hires_findgain.pro)
NAME:
hires_fit2darc
Version 1.1
PURPOSE:
To fit the arc lines identified in hires_fitarc as a fucntion of
their y-centroid and order number. The main routine is in
hires_fit2darc_work. The fit is a simple least-squares with one
round of rejection.
CALLING SEQUENCE:
hires_fit2darc, hires
INPUTS:
hires - HIRES structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
A fits file containing the 2D solution. Named something like
'Arcs/Fits/Arc_mb0539_fit2D.fits'
OPTIONAL KEYWORDS:
NOCOEFF - Number of coefficients to use in the x-direction
(default: 6 for blue, 7 for red)
NYCOEFF - Number of coefficients to use in the y-direction
(default: 4)
/CLOBBER - Overwrite any previous solution
/DEBUG - debug
/CHKRES - Plot the residuals
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_fit2darc, hires, 1.0
PROCEDURES/FUNCTIONS CALLED:
hires_fit2darc_work
REVISION HISTORY:
28-Feb-2003 Written by SB
18-Apr-2003 Revised by JXP
(See pro/Arcs/hires_fit2darc.pro)
NAME:
hires_fitarc
Version 1.1
PURPOSE:
To identify and centroid arc lines in each order. There is
actually no fitting done at this stage other than to reject bad
lines. The main program calls x_fitarc as its driver.
The algorithm x_fitarc does the following:
1) Input the arc image from hires_mkarc
2) Input an archived arc solution appropriate to the chip
3) Extract 1D (boxcar) spectra down each order :: extract_arc
4) Cross correlate (FFT) against the archived 1D arc spectrum,
this gives the order number and the pixel offset
5) Automatically identify a set of lines (x_templarc)
6) Perform a low order fit to these lines
7) Reidentify all lines with this fit and refit
8) Write arc solutions (one per order) to a fits file
9) If the orders extend beyond the archived solution, attempt to
extrapolate to the remaining orders. The idea is to use the
known wavelengths from the good orders to extrapolate a guess at
the solution. Then use this guess to peak up on the arc lines in
these additional orders.
CALLING SEQUENCE:
hires_fitarc, hires, setup, obj_id, [chip], /INTER, LINLIST=, /CHK, /CLOBBER,
SIGREJ=, /DEBUG, IORDR=, /PINTER
INPUTS:
hires - HIRES structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
IDL fit file (one per order) (e.g. Arcs/ArcECH_##fit.idl)
OPTIONAL KEYWORDS:
/PINTER - Perform fit for pre-identified lines
/INTER - Identify lines interactively and then fit
LINLIST - Arc line list (default: $XIDL_DIR/Spec/Arcs/Lists/hires_thar.lst
/CHK - Manually check steps along the way
/DEBUG - Debugging
SIGREJ= - Rejection sigma for outliers in arc line fitting
(default: 2.)
IORDR - Initial order for analysis
/CLOBBER - Overwrite previous fits
SHFTPRM= - Fit structure for shifting the orders of the arc
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_fitarc, hires, 1, 1
hires_fitarc, hires, 1, /clobb, arcfil='Arcs/Arc_B0171.fits'
PROCEDURES/FUNCTIONS CALLED:
x_fitarc
REVISION HISTORY:
20-Feb-2005 Created by JXP (based on mike_fitarc)
(See pro/Arcs/hires_fitarc.pro)
NAME:
hires_fitscatt
Version 1.2
PURPOSE:
Fit scattered light image to the light in the order gaps
CALLING SEQUENCE:
hires_fitscatt, img, ivar, ordr_str, chip
INPUTS:
RETURNS:
OUTPUTS:
A fit to the scattered light
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
PROCEDURES/FUNCTIONS CALLED:
x_fitgap
x_ordermask
REVISION HISTORY:
02-Sep-2005 Written by JXP
(See pro/Skysub/hires_fitscatt.pro)
NAME:
hires_fittflat
Version 1.1
PURPOSE:
To create a 2D solution which describes the order curvature. This
solution is derived from the individual traces created by
hires_trcflat and saved within the Trace structure. The 2D fitting
algorithm is a simple least-squares algorithm. The code then
attempts to extrapolate the solution for orders which are partially
on the CCD. The code then makes a guess for the physical order
number which is not particularly accurate right now. Finally, the
order structure (a key input for the HIRES pipeline) is written to
disk.
--- The code primarily calls x_fittflat for everything
CALLING SEQUENCE:
hires_fittflat, hires, setup, [chip], /DEBUG, INNY=, INNT=, LHEDGE=,
/CLOBBER
INPUTS:
hires - HIRES structure
setup - Setup identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
One normalized flat per slit width
OPTIONAL KEYWORDS:
INNY -- Number of coefficients for fitting in vertical
direction. (Default: 7)
INNT -- Number of coefficients for fitting in horizontal
direction. (Default: 6)
/DEBUG -- Turn debugging on
LHEDG -- Used primarily for debugging
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_fittflat, hires, 1, 1
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
28-Feb-2003 Written by SB
18-Apr-2003 Revised by JXP
(See pro/Flat/hires_fittflat.pro)
NAME:
hires_fittrcarc
Version 1.1
PURPOSE:
To fit the slope of the arc lines as a function of order number
and y position on the CCD. This information is then used to
construct a 2D wavelength image. The fitting routine is the usual
least-squares algorithm with two rounds of rejection.
CALLING SEQUENCE:
INPUTS:
hires - MIKE structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
Fits file with the coefficients of the 2D fit. Filename like
'Arcs/TRC/Arc_mb0539_F.fits'
OPTIONAL KEYWORDS:
/CHK -- Plots residuals
/CLOBBER -- Overwrite previous solution
/ORDRCLOB -- Overwrite arc_m in the order structure
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
PROCEDURES/FUNCTIONS CALLED:
hires_fittrcarc_work -- Main driver
hires_getfil
REVISION HISTORY:
24-Feb-2005 Written by JXP
(See pro/Arcs/hires_fittrcarc.pro)
NAME:
hires_flux
Version 1.1
PURPOSE:
Fluxes the spectrum using a standard star calibration. Default
is to use the one in CALIBS which is probably good enough for
relative fluxing. Definitely not good enough for absolute.
CALLING SEQUENCE:
hires_flux, hires, setup, obj_id, chip, FLUXFIL=, /CLOBBER, /STD
INPUTS:
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
chip - Blue (1) Green (2) or Red (3)
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
FLUXFIL - File name of standard star for fluxing (default:
$MIKE_DIR/pro/Std/Archive/sens_blue#.fits)
/STD - Extraction should be set for a standard star
/BOXCAR - Flux data from a Boxcar extraction
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_flux, hires, obj_id, /CLOBBER
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
02-Sep-2005 JXP
(See pro/Flux/hires_flux.pro)
NAME:
hires_fntobj
Version 1.1
PURPOSE:
Identify the object within the slit (single object) and trace it
along each order. The code rectifies each order, collapses it
and looks for the object. IF it finds it in >7 orders then it
peaks up on the object. Otherwise, it guesses the object is at
the center of the order. It then uses xy2tracset (trace_crude)
to trace the object along each order individually. Finally, it
performs a PCA analysis on the trace_crude coefficients to create
a smoothed (pseudo-2D) solution for the trace. The code outputs
an object structure which includes the trace and other info.
CALLING SEQUENCE:
hires_fntobj, hires, setup, obj_id, chip, [exp], /STD, /CHK [v1.0]'
INPUTS:
hires - MIKE structure
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
chip - Blue (1) or Red (2) chip
[exp] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
Object structure (MIKEOBJSTRCT) including the trace and other information
regarding the object. This structure is then filled up with the 1D
spectrum, etc.
OPTIONAL KEYWORDS:
/STD - Find object for standard star
/CHK - Show diagnostics of the code performance
/NOCLOB - Do not clobber existing files (default: clobber)
/DEBUG - Debug
OBJAPER - Set aperture to mask for sky subtraction (default: 20
unbinned pixels for obj, 26 for STD)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_fntobj, hires, 1L, 1L, /CHK,
PROCEDURES/FUNCTIONS CALLED:
hires_rectify
find_npeaks
hires_fweight
hires_fntobj_off
trace_crude
hires_basis
REVISION HISTORY:
23-Sep-2003 Written by JXP (combined aspects of fndobj with trcobj)
10-Nov-2003 Changed fntobj_off, SMB
(See pro/Object/hires_fntobj.pro)
NAME:
hires_getarcfil
Version 1.1
PURPOSE:
Runs through all of the Arc processing steps in one go.
Can be used to process a set of arcs for a given object or all
of the arcs from a given night.
This file also contains hires_allarc_sngl which can be used to
fully process a single arc image. In fact, if the keyword /ALL is
used, then hires_allarc simply loops through all of the arcs calling
hires_allarc_sngl for each one.
CALLING SEQUENCE:
hires_allarc, hires, setup, [chip], /CHK, /CLOBBER, /INDX
INPUTS:
hires - MIKE structure
setup - Integer defining setup OR an array of index values to
process
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
A series of files related to Arc calibration
OPTIONAL KEYWORDS:
/CLOBBER - Overwite any previous files
/CHK - Present GUIs to show results of fitting, etc.
/PINTER - Perform fit for pre-identified lines
/INDX - Treat setup as an array of index values to process
OPTIONAL OUTPUTS:
FITS= - File to write hires structure to (default: 'strct.fits')
ADDITIONAL KEYWORDS TO MIKE_ALLARC_SNGL:
/NOIMG - Do not create arc image
/NOWAV - Do not fit the arc lines (ie. only do tracing)
COMMENTS:
EXAMPLES:
hires_allarc, hires, 1L, 1L, /CHK, /CLOBBER
hires_allarc, hires, [104L, 107L], /INDX
rslt = hires_allarc_sngl('Raw/mb0539.fits', 1, 1, /PINTER)
PROCEDURES/FUNCTIONS CALLED:
hires_fitarc
hires_fit2darc
hires_tracearc
hires_fittrcarc
hires_mkaimg
REVISION HISTORY:
15-Aug-2003 Written by JXP
Usage:
(See pro/Arcs/hires_getarcfil.pro)
NAME:
hires_getfil
Version 1.1
PURPOSE:
Pass back a structure and/or filename for a specified file type in
the MIKE code.
CALLING SEQUENCE:
rslt = hires_getfil('type', [setup], CHIP=, /NAME, SUBFIL=, CHKFIL=,
SZ=, INDX=, FIL_NM=, HEAD=)
INPUTS:
[setup] - Setup identifier
RETURNS:
Structure, image, name, etc.
OUTPUTS:
OPTIONAL KEYWORDS:
/name -- Only return resolved name (string)
CHKFIL -- Value equal to the number of files matching name
SZ -- Image size
SUBFIL -- Image name generally used to parse the root name of the
image (e.g. 'Arcs/arc_mb0539.fits'). Required in
many cases.
CHIP -- Specify camera: Blue (1) or Red (2)
INDX -- Image extension in the fits file (generally 0, 1, or 2)
OPTIONAL OUTPUTS:
FIL_NM -- Filename of the file
HEAD -- Image header
COMMENTS:
EXAMPLES:
ordr_str = hires_getfil('ordr_str', 1, CHIP=1)
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP
(See pro/General/hires_getfil.pro)
NAME:
hires_getpixflat
Version 1.1
PURPOSE:
Pass back a structure and/or filename for a specified file type in
the MIKE code.
CALLING SEQUENCE:
rslt = hires_getfil('type', [setup], CHIP=, /NAME, SUBFIL=, CHKFIL=,
SZ=, INDX=, FIL_NM=, HEAD=)
INPUTS:
[setup] - Setup identifier
RETURNS:
Structure, image, name, etc.
OUTPUTS:
OPTIONAL KEYWORDS:
/name -- Only return resolved name (string)
CHKFIL -- Value equal to the number of files matching name
SZ -- Image size
SUBFIL -- Image name generally used to parse the root name of the
image (e.g. 'Arcs/arc_mb0539.fits'). Required in
many cases.
CHIP -- Specify camera: Blue (1) or Red (2)
INDX -- Image extension in the fits file (generally 0, 1, or 2)
OPTIONAL OUTPUTS:
FIL_NM -- Filename of the file
HEAD -- Image header
COMMENTS:
EXAMPLES:
flg = hires_getpixflat(chip, cbin, rbin, crossd, flat)
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP
(See pro/General/hires_getpixflat.pro)
NAME:
hires_headid
Version 1.1
PURPOSE:
Guess the type of MIKE image based on exposure time, counts,
and other characteristics of the image.
CALLING SEQUENCE:
guess = hires_headid(data, xbinguess, ybinguess, $
filename=img[q], hdr=head, /silent)
INPUTS:
data - 2D image (generally set to 0 and read from filename)
RETURNS:
Image type:: 'UNK', 'BAD', 'ZRO', 'ARC', 'TFLT', 'TFLT', 'STD',
'OBJ', 'MFLT', 'TWI'
OUTPUTS:
OPTIONAL KEYWORDS:
FILENAME - Name of the image to be considered
XBIN - x binning
YBIN - y binning
SILENT - Suppress print statements
SATURATED - Saturation level (default = 50000.)
OPTIONAL OUTPUTS:
HDR - Image header if filename specified
GUESS_EXPTIME -- Guess of exposure time based on CR hits
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
guess = hires_headid(data, xbin, ybin, filename='file')
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
??-??-2003 Written by SB
(See pro/General/hires_headid.pro)
NAME:
hires_mkaimg
Version 1.1
PURPOSE:
Given the 2D solution for the slope of the lines as a function of
position this code creates a wavelength image (i.e. assigns a
unique wavelength to each pixel in each order). The xoffset is
input in order to properly determine the edges of each order. A
simple spline interpolation is used to determine the values.
CALLING SEQUENCE:
hires_mkaimg, hires, setup, [chip], /CHK, /CLOBBER
INPUTS:
hires - MIKE structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
2D wavelength image with name like 'Arcs/Arc_mb0439I.fits'
OPTIONAL KEYWORDS:
/CLOBBER - Overwrite previous image
/CHK - Display the final image
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_mkaimg, hires, setup, obj_id
PROCEDURES/FUNCTIONS CALLED:
hires_getfil
REVISION HISTORY:
15-May-2003 Written by SB
(See pro/Arcs/hires_mkaimg.pro)
NAME:
hires_mkascii
Version 1.0
PURPOSE:
Deletes OV images
CALLING SEQUENCE:
hires_delov, hires, indx
INPUTS:
hires - ESI structure
indx - Index numbers of frames to delete
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_writefits, hires, indx
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
08-Sep-2005 Written by JXP
(See pro/Spec/hires_mkascii.pro)
NAME:
hires_mktempl
Version 1.1
PURPOSE:
CALLING SEQUENCE:
hires_arctempl, hires, setup, obj_id, [chip], /INTER, LINLIST=, /CHK, /CLOBBER,
SIGREJ=, /DEBUG, IORDR=, /PINTER
INPUTS:
hires - MIKE structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
IDL fit file (one per order) (e.g. Arcs/ArcECH_##fit.idl)
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_mktempl, hires, 1, 1
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
22-Aug-2005 Created by JXP
(See pro/Arcs/hires_mktempl.pro)
NAME:
hires_mktflat
Version 1.1
PURPOSE:
Combines all flats for a given setup into one final image.
The images are first bias subtracted using hires_subbias.
The images are median combined after scaling by the median after
iteratively rejecting bad pixels. The image and its inverse
variance array are written to one fits file. Because of the
thermal gradients, it is highly recommended that one use
only a coeval set of trace flats.
CALLING SEQUENCE:
hires_mktflat, hires, setup, [chip], /SVOV, /REDOOV, /CLOBBER
INPUTS:
hires - HIRES structure
setup - Setup identifier
[chip] - Blue (1), Green (2), Red (3), or multiple (Default:
[1,2,3L])
RETURNS:
OUTPUTS:
One normalized flat per setup and side
(e.g. 'Flats/Flat/_B_01_T.fits.gz')
OPTIONAL KEYWORDS:
/REDOOV - Overwrite OV files if they exist for the flats
/SVOV - Save the OV files created during this step
/CLOBBER - Overwrite the final fits file
/USEBIAS - Use the bias frame in bias subtraction
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_mktflat, hires, 1.0
PROCEDURES/FUNCTIONS CALLED:
hires_subbias
xcombine
hires_delov
REVISION HISTORY:
17-Apr-2003 Written by JXP
(See pro/Flat/hires_mktflat.pro)
NAME:
hires_nrmflat
Version 1.1
PURPOSE:
To normalize the flat (remove the blaze) to create an image useful
for pixel-to-pixel corrections. Ideally, I recommend you use one
of the archived flat frames as the flats created here have the
following problems:
1. They fail at the slit edges
2. They contain scattered light which cannot be removed
3. Large chip defects cause more trouble
CALLING SEQUENCE:
hires_nrmflat, hires, setup, [side], /CHK,
INPUTS:
hires - MIKE structure
setup - Setup identifier
[side] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
A normalized flat image
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_nrmflat, hires, 1
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
(See pro/Flat/hires_nrmflat.pro)
NAME:
hires_objcr
Version 1.1
PURPOSE:
Flags CRs given 2 or more object images.
CALLING SEQUENCE:
hires_objcr, hires, setup, obj_id, chip, [iexp]
INPUTS:
hires - MIKE structure
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
side - Blue (1) and/or Red (2) side (Default: [1L,2L])
[iexp] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
flat - fits file in the dir Flats named 'Flat_##.fits'
where ## is the mask_id value
VAR - Variance in the flat (in electrons)
OPTIONAL KEYWORDS:
SVOV - save ov files
/NOFITS - No FITS output
RTIO - Ratio CR must exceed to be flagged (default: 9)
OPTIONAL OUTPUTS:
COMMENTS:
Algorithm for 3 or more images is not well tested.
It would be nice to add a GROW option.
EXAMPLES:
hires_objcr, hires, setup, obj_id, chip,
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
19-Aug-2003 Written by JXP
(See pro/Object/hires_objcr.pro)
NAME:
hires_ordermask
Version 0.1
PURPOSE:
Returns a integer image which identifies each pixel with a given order
or inter-order gap.
CALLING SEQUENCE:
maskimage = hires_ordermask(ncol, nrow, ordr_str, trim=trim)
(note: it's a little silly to pass ncol and nrow, but had no better
idea at the time. I should have just passed hires structure,
but it doesn't really need it to run.)
INPUTS:
ncol - number of columns in image
nrow - number of rows
ordr_str - Structure array describing order format
RETURNS:
OUTPUTS:
An [NCOL,NROW] image with each pixel exclusively assigned to an order or gap
OPTIONAL KEYWORDS:
trim - The buffer included in each order (default 0. pixels).
Increasing trim increases the width of each order!
OPTIONAL OUTPUTS:
COMMENTS:
Crude routine to make a map of order placement
Orders fall at positive Maps [1...nord]
Gaps are marked with [-1 ... -NGAP]
Pixel leftward of 1st order or rightward of last order in
ordr_str are set to 0
EXAMPLES:
maskimage = hires_ordermask(ncol, nrow, ordr_str, trim=trim)
PROCEDURES/FUNCTIONS CALLED:
gap_index (internal routine to find those gaps!)
REVISION HISTORY:
15-Jul-2003 Checked in by SB
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
gap_index jumps through hoops to find the list of image indices which
lie between lhedg <= column <= rhedg
(See pro/General/hires_ordermask.pro)
NAME:
hires_parsehdu
Version 1.1
PURPOSE:
Guess the type of MIKE image based on exposure time, counts,
and other characteristics of the image.
CALLING SEQUENCE:
guess = hires_headid(data, xbinguess, ybinguess, $
filename=img[q], hdr=head, /silent)
INPUTS:
data - 2D image (generally set to 0 and read from filename)
RETURNS:
Image type:: 'UNK', 'BAD', 'ZRO', 'ARC', 'IFLT', 'TFLT', 'STD',
'OBJ', 'MFLT', IFLT', 'TWI'
OUTPUTS:
OPTIONAL KEYWORDS:
FILENAME - Name of the image to be considered
XBIN - x binning
YBIN - y binning
SILENT - Suppress print statements
SATURATED - Saturation level (default = 50000.)
OPTIONAL OUTPUTS:
HDR - Image header if filename specified
GUESS_EXPTIME -- Guess of exposure time based on CR hits
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
guess = hires_headid(data, xbin, ybin, filename='file')
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP
(See pro/General/hires_parsehdu.pro)
NAME:
hires_pixflat
Version 1.1
PURPOSE:
This set of routines takes a series of flats observed through the
diffuser and creates a normalized Flat used to correct
pixel-to-pixel response variations. A principal challenge with
MIKE in its current state (April 2004) is that it is difficult to
get sufficient counts on the blue chip.
hires_pixflat :: The main routine simply does some basic
accounting, organizes bias subtraction and performs I/O.
hires_mkflat_work :: Accepts the name(s) of a series of OV
subtracted milky flats. It then:
1. Opens the file and creates an inverse variance array
2. Takes out the low order variation in the image (lo_interp)
3. Performs a series of medians along the columns rejecting bad
pixels (replace by local mean).
4. If multiple images were input, they are stacked with
rejection and the final image is returned
CALLING SEQUENCE:
hires_pixflat, hires, setup, [side]
INPUTS:
hires - MIKE structure
setup - Setup identifier
[side] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
One normalized flat per setup per side with names like
'Flats/Flat_B_01_M.fits.gz'
OPTIONAL KEYWORDS:
/CLOBBER - Overwrite Output MilkyFlat
/OVCLOB - Overwrite OV files if they exist for the flats
/SVOV - Save the OV files created during this step
/USEBIAS - Use bias frame in OV subtraction
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_pixflat, hires, 1
PROCEDURES/FUNCTIONS CALLED:
hires_getfil
hires_subbias
hires_pixflat_work
REVISION HISTORY:
16-May-2003 Adapted by JXP from existing programs by SB
24-Feb-2004 Switched to a series of median/linear interpolations (SB)
(See pro/Flat/hires_pixflat.pro)
NAME:
hires_proc
Version 1.0
PURPOSE:
Process a raw data frame. Bias subtract and flatten. Output is
written in Final/ and is a mutli-extension fits file.
Extension-0 is the processed image, Extension-1 is the inverse
variance.
CALLING SEQUENCE:
There are several ways to call hires_proc
hires_proc, hires, indx [processes the image with index=indx]
hires_proc, hires, SETUP=1, OBJ=4 [processes images with setup=1 and
obj_id=4]
rslt = hires_proc_sngl('Rawfil') [process a single image]
INPUTS:
hires - HIRES structure
[indx] - Index (or indices) of the image(s) in the HIRES
structure to process
RETURNS:
OUTPUTS:
Fully processed image
OPTIONAL KEYWORDS:
/CLOBBER - Clobber existing image
SETUP - Setup number
EXP - Exposure numbers
OBJ - Obj_id value
/ARC - Identifies the image as an Arc explicitly. This is
important for bias subtraction on the red chip.
/NOFLAT - Do not flatten
FLATFIL - Name of flat file to use.
/SVOV - Save the OV subtracted image
/REDOOV - Overwrite any existing OV images
IOUTFIL - Name for output file (array for mult
/STD - Processes standard stars corresponding to an input SETUP
OPTIONAL OUTPUTS:
COMMENTS:
The inverse variance is given this set of values in an attempt to
deal with the Poisson limit
ivar = 1.0/(abs(img * gain - sqrt(2.0)*readno) + readno^2 )
EXAMPLES:
hires_proc, hires, [20L,21L], /CLOBBER
PROCEDURES/FUNCTIONS CALLED:
hires_proc_work
hires_subbias_sngl
hires_getfil
hires_delov
REVISION HISTORY:
30-Apr-2002 Written by JXP
19-Aug-2003 Added work routine
20-Feb-2005 Taken from mike_proc
(See pro/General/hires_proc.pro)
NAME:
hires_procarc
Version 1.1
PURPOSE:
Process (bias subtract, flatten) the arc files. In addition, the
code first calls hires_arcxyoff which uses a 2D FFT to determine
the offset between the Template Arc and the current arc due to
thermal expansion in the instrument.
This file also includes the routine hires_procarc_sngl which
allows the processing of a single Arc image given the filename of
the Raw image.
CALLING SEQUENCE:
hires_procarc, hires, setup, obj_id, [chip], ATEMPL=, /CLOBBER,
FLATFIL=
INPUTS:
hires - MIKE structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
One processed, combined Arc Image (e.g. Arcs/Arc_mb0539.fits)
OPTIONAL KEYWORDS:
/CLOBBER - Overwrite exisiting arc image
ATEMPL -- Index of the Template Arc image (default: 0L)
FLATFIL -- Filename of the milky flat (pixel to pixel correction)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_procarc, hires, 1, 1, 1, /CLOBBER
PROCEDURES/FUNCTIONS CALLED:
hires_getfil
hires_arcxyoff
hires_proc
REVISION HISTORY:
13-Aug-2003 Written by JXP
(See pro/Arcs/hires_procarc.pro)
NAME:
hires_qckrdx
Version 1.1
PURPOSE:
Examines the Kast IDL structure, checks for appropriate
Flats and Arcs and then outputs a summary ASCII file.
CALLING SEQUENCE:
hires_qckrdx, hires, OUTFIL=
INPUTS:
hires -- Kast IDL structure
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OUTFIL= -- Name of ASCII file (default: hires_summ.txt')
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_qckrdx, 'hires0023.fits',
['hires0030.fits','hires0031.fits'], 'hires0082.fits', CHIP=1
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
01-May-2005 Written by JXP
(See pro/General/hires_qckrdx.pro)
NAME:
hires_rdxlog
Version 1.1
PURPOSE:
Creates and outputs a structure for a series of MIKE images.
This structure organizes the data for the night and is used
to run most of the programs in the MIKE package. It will
attempt to identify the type of object using the algorithm
(hires_autoid). It also parses the header for information related
to exposure time, RA,DEC, etc. Finally, the code calculates the
gain for pairs of Milky flat exposures with the routine
hires_gain. At present these gain values are not used.
Use hires_setgain to set the values [highly recommended].
See hiresstrct__define.pro for all of the tags of the hires structure.
CALLING SEQUENCE:
hires_strct, struct, LIST=, /NOMKDIR, /NOFILE, OUTFIL=, /EDIT, FILE_LIST=
INPUTS:
By default the program examines all of the files with the form
*b####.fits in the Raw/ directory.
RETURNS:
OUTPUTS:
struct - IDL structure based on the MIKE images
OPTIONAL KEYWORDS:
LIST - Image list: e.g. 'gd_files.lst'
NOMKDIR - Suppress the creation of sub directories (not
recommended)
EDIT - Edit the final structure with the GUI
OUTFIL - Name of fits output file (default = hiresstrct.fits)
FILE_LIST - String Array of all input filenames
OPTIONAL OUTPUTS:
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
hires_strct, nght1_strct
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP
(See pro/General/hires_rdxlog.pro)
NAME:
hires_redux
Version 1.0
PURPOSE:
Calls various routines to analyse the data
CALLING SEQUENCE:
hires_redux, wfccd, maskid, expsr, XSIZE=, YSIZE=
INPUTS:
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_redux, hires
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
02-May-2005 Written by JXP
(See pro/General/hires_redux.pro)
NAME:
hires_rslvall
Version 1.1
PURPOSE:
Resolves a number of key codes for MIKE redux
CALLING SEQUENCE:
hires_rslvall
INPUTS:
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_rslvall
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
19-Aug-2003 Written by JXP
(See pro/General/hires_rslvall.pro)
NAME:
hires_setarcfil
Version 1.1
PURPOSE:
Set the arc file name
CALLING SEQUENCE:
hires_setarcfil, hires, setup
INPUTS:
hires - Raw arc file used to set the arc_m values
setup - Integer defining setup
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
ADDITIONAL KEYWORDS TO MIKE_ALLARC_SNGL:
COMMENTS:
EXAMPLES:
hires_setarcfil, hires, 1
PROCEDURES/FUNCTIONS CALLED:
hires_getfil
REVISION HISTORY:
28-Sep-2005 Written by JXP
Usage:
(See pro/Arcs/hires_setarcfil.pro)
NAME:
hires_setarcm
Version 1.1
PURPOSE:
Run through the necessary steps to set the arc_m values in the
order structure. This seperate routine was created to avoid the
high level of confusion occuring in hires_allarc.
CALLING SEQUENCE:
hires_setarcm, arc_fil, setup, chip
INPUTS:
arc_fil - Raw arc file used to set the arc_m values
setup - Integer defining setup
chip - Blue (1) or Red (2)
RETURNS:
OUTPUTS:
A series of files related to Arc calibration
OPTIONAL KEYWORDS:
/PINTER - Perform fit for pre-identified lines
OPTIONAL OUTPUTS:
ARC_FIL= - Name of processed arc
XYOFF= - Offset fit info
ADDITIONAL KEYWORDS TO MIKE_ALLARC_SNGL:
COMMENTS:
EXAMPLES:
hires_setarcm, 'Raw/hires_mb0032', 1, 1
PROCEDURES/FUNCTIONS CALLED:
hires_procarc
hires_alignarc
hires_fitarc
hires_fit2darc
hires_tracearc
hires_fittrcarc
REVISION HISTORY:
18-Aug-2004 Written by JXP
Usage:
(See pro/Arcs/hires_setarcm.pro)
NAME:
hires_setgainrn
Version 1.1
PURPOSE:
Guess the type of MIKE image based on exposure time, counts,
and other characteristics of the image.
CALLING SEQUENCE:
guess = hires_headid(data, xbinguess, ybinguess, $
filename=img[q], hdr=head, /silent)
INPUTS:
data - 2D image (generally set to 0 and read from filename)
RETURNS:
Image type:: 'UNK', 'BAD', 'ZRO', 'ARC', 'IFLT', 'TFLT', 'STD',
'OBJ', 'MFLT', IFLT', 'TWI'
OUTPUTS:
OPTIONAL KEYWORDS:
FILENAME - Name of the image to be considered
XBIN - x binning
YBIN - y binning
SILENT - Suppress print statements
SATURATED - Saturation level (default = 50000.)
OPTIONAL OUTPUTS:
HDR - Image header if filename specified
GUESS_EXPTIME -- Guess of exposure time based on CR hits
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
hires_setgainrn, hires, idx, ccdgain
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP (These values are only good for after
10/27/2004)
22-Aug-2005 Updated gain for pre-Oct 2004 based on my own
measurements
(See pro/General/hires_setgainrn.pro)
NAME:
hires_setup
Version 1.1
PURPOSE:
Examines the Kast IDL structure, checks for appropriate
Flats and Arcs and then outputs a summary ASCII file.
CALLING SEQUENCE:
hires_setup, hires, OUTFIL=
INPUTS:
hires -- Kast IDL structure
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OUTFIL= -- Name of ASCII file (default: hires_summ.txt')
/KEEPSET -- Dont modify the setup numbers (useful to reset the
arcs)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_setup, hires
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
01-Mar-2003 Written by JXP
(See pro/General/hires_setup.pro)
NAME:
hires_skysub
Version 1.2
PURPOSE:
Sky Subtract image and add sky subtracted frame to the final
image (e.g. Final/f_hires0020.fits). The program also outputs
information related to the sky fit in the Sky directory. The
user has control over which order to subtract (ORDR=), the
wavelength image to use (AIMG=). The program preforms the
following steps:
1. Offset the Order structure by the appropriate shift
2. Subtract scattered light (hires_fitgap)
-- LOOP ON ORDERS --
3. After masking the object, the code finds the sky pixels and
normalizes them by the slit profile.
4. It bspline fit to the sky
5. It assesses the fit and adds in breakpoints in a somewhat
smart way.
6. It performs a second bspline fit
7. The coefficients of the fit are saved and the image is
subtracted
8. The code compares the extracted sky spectrum against the UVES
sky spectrum to guess at a shift. This is saved to the Object
structure.
-- END OF LOOP
9. The final sky subtracted image is written to the fits file
(extension #2)
CALLING SEQUENCE:
hires_skysub, hires, setup, obj_id, side, [exp], /CHK, /STD, ORDR=,
AIMG=, /USEOLD, /FCHK
INPUTS:
hires - MIKE structure
setup - Setup ID
obj_id - Object ID (e.g. 1L) (or STD index if /STD set)
side - Blue (1) or Red (2) side
[exp] - Exposure frames (e.g. [0L, 1L])
RETURNS:
OUTPUTS:
A sky subtracted image added as extension #2 to the fits file.
A file in the directory Sky/ describing the fit
OPTIONAL KEYWORDS:
/STD - Sky subtract standard star
/CHK - Show steps along the way
AIMG= - Use alternate Wavelength map for sky subtraction
(string filename)
ORDR= - Sky subtract a single order only (e.g. [5L,5L])
/CLOBBER - Overwrite any previos sky image
/USEOLD - Overwrite only the new orders into the old sky sub image
/FCHK - Show the final sky subtracted image
OPTIONAL OUTPUTS:
SCATTERED_LIGHT= -- Scattered light image. It may be useful to
save and use this if you are subtracting individual
orders
COMMENTS:
EXAMPLES:
hires_skysub, hires, 1L, 1L, 1L, /FCHK
PROCEDURES/FUNCTIONS CALLED:
hires_fitgap
hires_ordermask
bspline_iterfit
hires_getfil
hires_skyshift
hires_skysub_write
REVISION HISTORY:
16-May-2003 Written by JXP
??-2003 Modified extensively by SMB
26-Jun-2004 Update arc shifting
(See pro/Skysub/hires_skysub.pro)
NAME:
hires_slitflat
Version 1.1
PURPOSE:
Stores slit profile and gradient along each order from twilight flats.
This routine is critical for performing ideal sky subtraction,
especially given the short slit length. The following steps are
performed in hires_slitflat_work:
1. Fit and subtract the scattered light in the twilight flat
2. Extract a boxcar profile down the center of the flat
3. Loop on orders
4. Calculate the slit angle at each pixel in the order
5. Calculate the Jacobian (DEPRECATED)
6. Fit a bspline to the profile
7. Run diagnsotics on the fit
8. Save the good ones to profile0 and profile1 tags
CALLING SEQUENCE:
hires_slitflat, hires, setup, chip, [/chk, /clobber]
INPUTS:
hires - MIKE structure
setup - Setup identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
Fills in the profile0 and profile1 tags in the Order structure
OPTIONAL KEYWORDS:
/CHK - Show the profiles and fits order by order
/CLOBBER - Clobber an previous work
TFLAT_FIL - Name for TFLAT file
RESIDUAL_FIL - Output name for Jacobian matrix
PROFILE_FIL - Output name for profile fits
DETILT - Remove a linear tilt from the Cross-section fit
NXBKT - Number of x breakpoints for scattered light fit
NYBKT - Number of x breakpoints for scattered light fit
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_slitflat, hires, 1
PROCEDURES/FUNCTIONS CALLED:
hires_ordermask
hires_fitgap
hires_qw
hires_slitflat_work
REVISION HISTORY:
??-??-2003 Written by SB
(See pro/Flat/hires_slitflat.pro)
NAME:
hires_slitlen
Version 1.1
PURPOSE:
Guess the type of MIKE image based on exposure time, counts,
and other characteristics of the image.
CALLING SEQUENCE:
guess = hires_headid(data, xbinguess, ybinguess, $
filename=img[q], hdr=head, /silent)
INPUTS:
data - 2D image (generally set to 0 and read from filename)
RETURNS:
Image type:: 'UNK', 'BAD', 'ZRO', 'ARC', 'IFLT', 'TFLT', 'STD',
'OBJ', 'MFLT', IFLT', 'TWI'
OUTPUTS:
OPTIONAL KEYWORDS:
FILENAME - Name of the image to be considered
XBIN - x binning
YBIN - y binning
SILENT - Suppress print statements
SATURATED - Saturation level (default = 50000.)
OPTIONAL OUTPUTS:
HDR - Image header if filename specified
GUESS_EXPTIME -- Guess of exposure time based on CR hits
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
hires_slitlen, hires, idx, ccdgain
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
23-Aug-2005 Written by JXP
(See pro/General/hires_slitlen.pro)
NAME:
hires_specplt
Version 1.0
PURPOSE:
Plots any array interactively
CALLING SEQUENCE:
hires_specplt, ydat, [head], XSIZE=, YSIZE=, TITLE=, WAVE=, LLIST=,
QAL=, ERR=, /GAL
INPUTS:
ydat - Values
[head] - Header
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
xsize - Draw window xsize (pixels)
ysize - Draw window ysize (pixels)
wave - wavelength array
ERR - Error array (fits or image)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_specplt, 'spec.fits'
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
23-Aug-2002 Written by JXP
(See pro/Spec/hires_specplt.pro)
NAME:
hires_strct
Version 1.1
PURPOSE:
Creates and outputs a structure for a series of MIKE images.
This structure organizes the data for the night and is used
to run most of the programs in the MIKE package. It will
attempt to identify the type of object using the algorithm
(hires_autoid). It also parses the header for information related
to exposure time, RA,DEC, etc. Finally, the code calculates the
gain for pairs of Milky flat exposures with the routine
hires_gain. At present these gain values are not used.
Use hires_setgain to set the values [highly recommended].
See hiresstrct__define.pro for all of the tags of the hires structure.
CALLING SEQUENCE:
hires_strct, struct, LIST=, /NOMKDIR, /NOFILE, OUTFIL=, /EDIT, FILE_LIST=
INPUTS:
By default the program examines all of the files with the form
*b####.fits in the Raw/ directory.
RETURNS:
OUTPUTS:
struct - IDL structure based on the MIKE images
OPTIONAL KEYWORDS:
LIST - Image list: e.g. 'gd_files.lst'
NOMKDIR - Suppress the creation of sub directories (not
recommended)
EDIT - Edit the final structure with the GUI
OUTFIL - Name of fits output file (default = hiresstrct.fits)
FILE_LIST - String Array of all input filenames
OPTIONAL OUTPUTS:
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
hires_strct, nght1_strct
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP
(See pro/General/hires_strct.pro)
NAME:
hires_subbias
Version 1.2
PURPOSE:
Remove bias from all exposures listed in the "hires" structure.
The main driver is hires_suboscan which strips the image of the
overscan region (see that program for a full
description). The hires_subbias routine will also remove an
archived bias image if requested.
CALLING SEQUENCE:
hires_subbias, hires, indx, /usebias, /nobiasrow, /clobber, /ARC,
/debug, BADROW=
INPUTS:
hires - MIKE structure
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
/NOBIASROW= if set, bias row is not used (normally, you should not use it)
/USEBIAS = use the bias image in addition to subtracting a fit to the
overscan columns (at right). The code first generates a
smoothed version of the bias image.
If you do this, you want to be sure the same options
were used in hires_mkbias (i.e. /nobiasrow )
Presently, this step is not recommended.
/CLOBBER = Overwrite existing OV files
/DEBUG -- Turn debug mode on
BADROW -- Rows identified as anomolous in the overscan region.
Generally the result of an electronics 'hiccup'.
OUTPUTS TO SNGL:
/NOFITS -- Do not write a fits file
OVIMG= -- Bias subtracted image
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_subbias, hires, indx, /usebias, /nobiasrow
PROCEDURES/FUNCTIONS CALLED:
hires_subbias_sngl -- Subroutine under hires_subbias. Uses most of
the keywords described above. Example:
rslt = hires_subbias_sngl('Raw/mb0020.fits',
chip)
hires_suboscan
REVISION HISTORY:
01-Feb-2005 Written by JXP (taken from mike_subbias)
(See pro/Bias/hires_subbias.pro)
NAME:
hires_test
Version 1.1
PURPOSE:
Reads in the first fits file in the directory with name
'hires_*.fits' and passes back the hires structure.
CALLING SEQUENCE:
hires = hires_ar(file)
INPUTS:
[file] - Filename (default: first file in list ./hires_*fits*)
RETURNS:
hires - MIKE structure
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires = hires_ar()
PROCEDURES/FUNCTIONS CALLED:
hires_rslvall
REVISION HISTORY:
13-Nov-2001 Written by JXP
03-Feb-2003 Polished (JXP)
(See pro/General/hires_test.pro)
NAME:
hires_tracearc
Version 1.1
PURPOSE:
To trace the arc lines in each order (individually) and fit a
straight line to each one. The following steps are taken:
1. Scattered light is removed from the image
2. All significant arc lines are identified (5 sigma)
3. trace_crude is used to trace the lines
4. trace_crude is reapplied to only those lines which are
entirely in the order
5. xy2traceset is used to fit a straight line to each arc line
6. Only the good lines are saved for 2D fitting in a structure
which is written to disk
CALLING SEQUENCE:
hires_tracearc, hires, setup, obj_id, [chip], /CLOBBER, INIO=
INPUTS:
hires - MIKE structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
all_xset -- A structure describing the fits to the arc lines
OUTPUTS:
OPTIONAL KEYWORDS:
INIO - Initial order (for debugging)
/CLOBBER - Overwrite previous fits
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_tracearc, hires, setup, obj_id
PROCEDURES/FUNCTIONS CALLED:
trace_crude
xy2traceset
x_echtracearc
REVISION HISTORY:
28-Apr-2003 Written by SB
(See pro/Arcs/hires_tracearc.pro)
NAME:
hires_trcflat
Version 1.1
PURPOSE:
This is mainly a frontend to x_trcflat. See that routine for
extensive (and the most recent) details
CALLING SEQUENCE:
hires_trcflat, hires, setup, [side], /CHK,
INPUTS:
hires - MIKE structure
setup - Setup identifier
[side] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
A structure containing the information for the order by order
fits. This structure is then fed to hires_fittflat to create a 2D
solution. Typical name: 'Flats/TStr_B_01.fits'
OPTIONAL KEYWORDS:
/CHK -- Check the order edges interactively (similar to INTER)
/INTER -- Determine the order edges interactively
SMSHROW -- Row where order edges are determined (default: 1/2 way
up the image)
THRESH -- Threshold for an order edge on the red side
(default: 100.)
/CLOBBER -- Overwrite the output structure
P_NSIG -- Number of sigma significance that an order edge should
have for the red side (default: 50.)
NSIG -- Number of sigma significance that an order edge should
have fo the blue side (default: 2.0)
MINFLAT -- Mininum counts in flat on blue side to use orders (100)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_trcflat, hires, 1.0
PROCEDURES/FUNCTIONS CALLED:
hires_trcflat_clean
hires_getfil
x_trcflat
REVISION HISTORY:
Feb-2005 Written by JXP
(See pro/Flat/hires_trcflat.pro)
NAME:
hires_tweakarc
Version 1.1
PURPOSE:
CALLING SEQUENCE:
hires_fitarc, hires, setup, obj_id, [chip], /INTER, LINLIST=, /CHK, /CLOBBER,
SIGREJ=, /DEBUG, IORDR=, /PINTER
INPUTS:
hires - HIRES structure
setup - Integer defining setup
obj_id - Object identifier
[chip] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
IDL fit file (one per order) (e.g. Arcs/ArcECH_##fit.idl)
OPTIONAL KEYWORDS:
/PINTER - Perform fit for pre-identified lines
/INTER - Identify lines interactively and then fit
LINLIST - Arc line list (default: $XIDL_DIR/Spec/Arcs/Lists/hires_thar.lst
/CHK - Manually check steps along the way
/DEBUG - Debugging
SIGREJ= - Rejection sigma for outliers in arc line fitting
(default: 2.)
IORDR - Initial order for analysis
/CLOBBER - Overwrite previous fits
SHFTPRM= - Fit structure for shifting the orders of the arc
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_fitarc, hires, 1, 1
PROCEDURES/FUNCTIONS CALLED:
x_fitarc
REVISION HISTORY:
Summer-2005 Created by JXP
(See pro/Arcs/hires_tweakarc.pro)
NAME:
hires_writefits
Version 1.0
PURPOSE:
Deletes OV images
CALLING SEQUENCE:
hires_delov, hires, indx
INPUTS:
hires - ESI structure
indx - Index numbers of frames to delete
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
hires_writefits, hires, indx
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
08-Sep-2005 Written by JXP
(See pro/General/hires_writefits.pro)
NAME:
hires_wrstrct
Version 1.1
PURPOSE:
Write the hires structure to a FITS file and write an ASCII summary
CALLING SEQUENCE:
hires_wrstrct, hires, /ANONLY, OUTFIL=, FITS=
INPUTS:
hires - An ESI structure
RETURNS:
OUTPUTS:
OPTIONAL KEYWORDS:
ANONLY - Only print files with flg_anly NE 0
OPTIONAL OUTPUTS:
OUTFIL= - Output file (default: 'hires.list')
FITS= - Name of fits output file (default: 'strct.fits')
COMMENTS:
EXAMPLES:
hires_wrstrct, hires, FITS='hires_13oct02.fits'
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
24-Jan-2005 Written by JXP
(See pro/General/hires_wrstrct.pro)
NAME:
mike_autoid
Version 1.1
PURPOSE:
Guess the type of MIKE image based on exposure time, counts,
and other characteristics of the image.
CALLING SEQUENCE:
guess = mike_autoid(data, xbinguess, ybinguess, $
filename=img[q], hdr=head, /silent)
INPUTS:
data - 2D image (generally set to 0 and read from filename)
RETURNS:
Image type:: 'UNK', 'BAD', 'ZRO', 'ARC', 'IFLT', 'TFLT', 'STD',
'OBJ', 'MFLT', IFLT', 'TWI'
OUTPUTS:
OPTIONAL KEYWORDS:
FILENAME - Name of the image to be considered
XBIN - x binning
YBIN - y binning
SILENT - Suppress print statements
SATURATED - Saturation level (default = 50000.)
OPTIONAL OUTPUTS:
HDR - Image header if filename specified
GUESS_EXPTIME -- Guess of exposure time based on CR hits
COMMENTS:
Need to do some consistency checks between red and blue side,
i.e. they should be the same type
EXAMPLES:
guess = mike_autoid(data, xbin, ybin, filename='file')
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
??-??-2003 Written by SB
(See pro/General/hires_autoid.pro)
NAME:
mike_crossarc
Version 1.1
PURPOSE:
Finds shift between saved template and current arc spectra.
CALLING SEQUENCE:
mike_crossarc, guessarc, cur_aspec, guess_spec, guess_fit, ordrs, $
ordr_shift, row_shift, chk=chk, sigrej=sigrej, /DEBUG
INPUTS:
guessarc - Filename of IDL save file with known wavelength solution
cur_aspec - Current extracted Arc spectra to be fit
obj_id - Object identifier
[side] - Blue (1), Red (2), or both [1,2L] (Default: [1,2L])
RETURNS:
OUTPUTS:
guess_spec - saved arc spectrum rebinned to match cur_aspec
guess_fit - polynomial wavelength fits in rebinned space
ordrs - Orders matching saved spectrum
ordr_shift - Order offset between template and current
row_shift - Pixel offset between template and current
OPTIONAL KEYWORDS:
/CHK - Manually check steps along the way
/DEBUG - Debugging
SIGREJ= - Rejection sigma for outliers in arc line fitting
(default: 2.)
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
PROCEDURES/FUNCTIONS CALLED:
restore
fft()
REVISION HISTORY:
2004 Written by SB
(See pro/Arcs/hires_crossarc.pro)
NAME:
x_wrechfspec
Version 1.0
PURPOSE:
Reads and writes the echfspec structure
CALLING SEQUENCE:
x_wrechfspec, echfspec, outfil, /READ
INPUTS:
wfstrct - WFCCD structure
RETURNS:
OUTPUTS:
wfarc - WFCCD arc structure (fits file)
OPTIONAL KEYWORDS:
OPTIONAL OUTPUTS:
COMMENTS:
EXAMPLES:
x_wrechfspec, echfspec, 'Extract/2015+657_ech.fits'
PROCEDURES/FUNCTIONS CALLED:
REVISION HISTORY:
08-Sep-2005 Written by JXP
(See pro/Spec/hires_wrfspec.pro)