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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)