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diff --git a/noao/imred/kpnocoude/doc/do3fiber.ms b/noao/imred/kpnocoude/doc/do3fiber.ms new file mode 100644 index 00000000..d572d035 --- /dev/null +++ b/noao/imred/kpnocoude/doc/do3fiber.ms @@ -0,0 +1,1413 @@ +.nr PS 9 +.nr VS 11 +.de V1 +.ft CW +.nf +.. +.de V2 +.fi +.ft R +.. +.de LS +.br +.in +2 +.. +.de LE +.br +.sp .5v +.in -2 +.. +.ND February 1993 +.TL +Guide to the Coude Three Fiber Reduction Task DO3FIBER +.AU +Francisco Valdes +.AI +IRAF Group - Central Computer Services +.K2 +.DY + +.AB +The \fBdo3fiber\fR reduction task is specialized for scattered light +subtraction, extraction, flat +fielding, and wavelength calibration of multifiber data in which some +fibers are used to take object spectra and other fibers are used to +take simultaneous arc spectra. A three fiber instrument of this +type (one object and two arc fibers) is available at the KPNO coude feed. +The default parameters are set for this configuration. +If there are a large number of fibers and fiber throughput and sky +fiber subtraction is needed the \fBdofiber\fR task should be used. +.LP +The \fBdo3fiber\fR task is a command language script which collects +and combines the functions and parameters of many general purpose tasks to +provide a single complete data reduction path. The task provides a degree +of guidance, automation, and record keeping necessary when dealing with +this type of multifiber data. +.AE +.NH +Introduction +.LP +The \fBdo3fiber\fR reduction task is specialized for scattered light +subtraction, extraction, flat +fielding, and wavelength calibration of multifiber data in which some +fibers are used to take object spectra and other fibers are used to +take simultaneous arc spectra. A three fiber instrument of this +type (one object and two arc fibers) is available at the KPNO coude feed. +The default parameters are set for this configuration. +If there are a large number of fibers and fiber throughput and sky +fiber subtraction is needed the \fBdofiber\fR task should be used. +.LP +The \fBdo3fiber\fR task is a command language script which collects +and combines the functions and parameters of many general purpose tasks to +provide a single complete data reduction path. The task provides a degree +of guidance, automation, and record keeping necessary when dealing with +this type of multifiber data. +.LP +The general organization of the task is to do the interactive setup steps +first using representative calibration data and then perform the majority +of the reductions automatically, and possibly as a background process, with +reference to the setup data. In addition, the task determines which setup +and processing operations have been completed in previous executions of the +task and, contingent on the \f(CWredo\fR and \f(CWupdate\fR options, skip or +repeat some or all the steps. +.LP +The description is divided into a quick usage outline followed by details +of the parameters and algorithms. The usage outline is provided as a +checklist and a refresher for those familiar with this task and the +component tasks. It presents only the default or recommended usage. Since +\fBdo3fiber\fR combines many separate, general purpose tasks the +description given here refers to these tasks and leaves some of the details +to their help documentation. +.NH +Usage Outline +.LP +.IP [1] 6 +The images are first processed with \fBccdproc\fR for overscan, +bias, and dark corrections. +The \fBdo3fibers\fR task will abort if the image header keyword CCDPROC, +which is added by \fBccdproc\fR, is missing. If the data processed outside +of the IRAF \fBccdred\fR package then a dummy CCDPROC keyword should be +added to the image headers; say with \fBhedit\fR. +.IP [2] +Set the \fBdo3fiber\fR parameters with \fBeparam\fR. Specify the object +images to be processed, the flat field image as the aperture reference and +the flat field, and one or more arc images. If there are many +object or arc spectra per setup you might want to prepare "@ files". +.IP [3] +Run the task. This may be repeated multiple times with different +observations and the task will generally only do the setup steps +once and only process new images. Queries presented during the +execution for various interactive operations may be answered with +"yes", "no", "YES", or "NO". The lower case responses apply just +to that query while the upper case responses apply to all further +such queries during the execution and no further queries of that +type will be made. +.IP [4] +The apertures are defined using the specified aperture reference image +which is usually a flat field in which both the object and arc fibers are +illuminated. The specified number of fibers are found automatically and +sequential apertures assigned. +.IP [5] +A query is given allowing the apertures to be interactively reviewed. +In this mode one may adjust the aperture widths as desired either +explicitly (:lower and :upper), with the cursor ('l' and 'u'), at a +particular flux level ('y'), or with an automatic algorithm ('z') +as described by \fBapresize\fR. To exit type 'q'. +.IP [6] +The fiber positions at a series of points along the dispersion are measured +and a function is fit to these positions. This may be done interactively to +adjust the fitting parameters. Not all fibers need be examined and the "NO" +response will quit the interactive fitting. To exit the interactive +fitting type 'q'. +.IP [7] +If scattered light subtraction is to be done the flat field image is +used to define the scattered light fitting parameters interactively. +If one is not specified then the aperture reference image is used for +this purpose. + +There are two queries for the interactive fitting. A graph of the +data between the defined reference apertures separated by a specified +buffer distance is first shown. The function order and type may be +adjusted. After quiting with 'q' the user has the option of changing +the buffer value and returning to the fitting, changing the image line +or column to check if the fit parameters are satisfactory at other points, +or to quit and accept the fit parameters. After fitting all points +across the dispersion another graph showing the scattered light from +the individual fits is shown and the smoothing parameters along the +dispersion may be adjusted. Upon quiting with 'q' you have the option +of checking other cuts parallel to the dispersion or quiting and finishing +the scattered light function smoothing and subtraction. + +If there is a throughput image then this is corrected for scattered light +noninteractively using the previous fitting parameters. +.IP [8] +If flat fielding is to be done the flat field spectra are extracted. The +average spectrum over all fibers is determined and a function is fit +interactively (exit with 'q'). This function is generally of sufficiently +high order that the overall shape is well fit. This function is then used +to normalize the individual flat field spectra. +The final response spectra are normalized to a unit +mean over all fibers. +.IP [9] +If dispersion correction is selected the first arc in the arc list is +extracted. The middle fiber is used to identify the arc lines and define +the dispersion function using the task \fBautoidentify\fR. The +\fIcrval\fR and \fIcdelt\fR parameters are used in the automatic +identification. Whether or not the automatic identification is +successful you will be shown the result of the arc line identification. +If the automatic identification is not successful identify a few arc +lines with 'm' and use the 'l' line list identification command to +automatically add additional lines and fit the dispersion function. Check +the quality of the dispersion function fit with 'f'. When satisfied exit +with 'q'. +.IP [10] +The remaining fibers are automatically reidentified. You have the option +to review the line identifications and dispersion function for each fiber +and interactively add or delete arc lines and change fitting parameters. +This can be done selectively, such as when the reported RMS increases +significantly. +.IP [11] +If the spectra are to be resampled to a linear dispersion system +(which will be the same for all spectra) default dispersion parameters +are printed and you are allowed to adjust these as desired. +.IP [12] +The object spectra are now automatically scattered light subtracted, + extracted, flat fielded, and dispersion corrected. +The reference apertures are first assigned +to the object spectra. If the \f(CWrecenter\fR option is set the apertures +will have a shift applied based on recentering the fiber profiles. +If the \f(CWedit\fR option is set you may review and modify +the aperture definitions interactively. Any new +arcs assigned to the object images are automatically extracted and +dispersion functions determined. A zero point wavelength correction +is computed from the arc fiber spectra and applied to the object spectrum. +.IP [13] +The option to examine the final spectra with \fBsplot\fR may be given. +To exit type 'q'. +.IP [14] +If scattered light is subtracted from the input data a copy of the +original image is made by appending "noscat" to the image name. +If the data are reprocessed with the \fIredo\fR flag the original +image will be used again to allow modification of the scattered +light parameters. + +The final spectra will have the same name as the original 2D images +with a ".ms" extension added. +.NH +Spectra and Data Files +.LP +The basic input consists of multifiber object and calibration spectra +stored as IRAF images. +The type of image format is defined by the +environment parameter \fIimtype\fR. Only images with that extension will +be processed and created. +There are two types of calibration images. These +are flat fields and comparison lamp arc spectra. The raw CCD images must +be processed to remove overscan, bias, and dark count effects. This is +generally done using the \fBccdred\fR package. +The \fBdo3fiber\fR task will abort if the image header keyword CCDPROC, +which is added by \fBccdproc\fR, is missing. If the data processed outside +of the IRAF \fBccdred\fR package then a dummy CCDPROC keyword should be +added to the image headers; say with \fBhedit\fR. +Flat fielding is generally +not done at this stage but as part of \fBdo3fiber\fR. If for some reason +the flat field or calibration arc spectra have separate exposures through +different fibers they may be simply added. +.LP +The assignment of arc calibration exposures to object exposures is +generally done by selecting the nearest in time and interpolating. +However, the optional \fIarc assignment table\fR may be used to explicitly +assign arc images to specific objects. The format of this file is +described in the task \fBrefspectra\fR. +.LP +The final reduced spectra are recorded in one, two or three dimensional IRAF +images. The images have the same name as the original images with an added +".ms" extension. Each line in the reduced image is a one dimensional +spectrum with associated aperture, wavelength, and identification +information. With a single object spectrum the image will be one dimensional +and with multiple object spectra the image will be two dimensional. +When the \f(CWextras\fR parameter is set the images will be three +dimensional (regardless of the number of apertures) and the lines in the +third dimension contain additional information (see +\fBapsum\fR for further details). These spectral formats are accepted by the +one dimensional spectroscopy tasks such as the plotting tasks \fBsplot\fR +and \fBspecplot\fR. +.NH +Package Parameters +.LP +The \fBkpnocoude\fR package parameters, shown in Figure 1, set parameters +affecting all the tasks in the package. Some of the parameters are not +applicable to the \fBdo3fiber\fR task. +.KS +.V1 + +.ce +Figure 1: Package Parameters for KPNOCOUDE + + I R A F + Image Reduction and Analysis Facility +PACKAGE = imred + TASK = kpnocoude + +(extinct= onedstds$kpnoextinct.dat) Extinction file +(caldir = onedstds$spec50cal/) Standard star calibration directory +(observa= observatory) Observatory of data +(interp = poly5) Interpolation type +(dispaxi= 2) Image axis for 2D images +(nsum = 1) Number of lines/columns to sum for 2D images + +(databas= database) Database +(verbose= no) Verbose output? +(logfile= logfile) Log file +(plotfil= ) Plot file + +(records= ) Record number extensions +(version= KPNOCOUDE V3: January 1992) + +.KE +.V2 +The observatory parameter is only required for data +without an OBSERVAT header parameter (currently included in NOAO data). +The spectrum interpolation type might be changed to "sinc" but with the +cautions given in \fBonedspec.package\fR. The dispersion axis parameter is +only needed if a DISPAXIS image header parameter is not defined. The other +parameters define the standard I/O functions. The verbose parameter +selects whether to print everything which goes into the log file on the +terminal. It is useful for monitoring what the \fBdo3fiber\fR task does. The +log and plot files are useful for keeping a record of the processing. A +log file is highly recommended. A plot file provides a record of +apertures, traces, and extracted spectra but can become quite large. +The plotfile is most conveniently viewed and printed with \fBgkimosaic\fR. +.NH +Processing Parameters +.LP +The \fBdo3fiber\fR parameters are shown in Figure 2. +.KS +.V1 + +.ce +Figure 2: Parameter Set for DO3FIBER + + I R A F + Image Reduction and Analysis Facility +PACKAGE = kpnocoude + TASK = do3fiber + +objects = List of object spectra +(apref = ) Aperture reference spectrum +(flat = ) Flat field spectrum +(arcs = ) List of arc spectra +(arctabl= ) Arc assignment table (optional) + +.KE +.V1 +(readnoi= RDNOISE) Read out noise sigma (photons) +(gain = GAIN) Photon gain (photons/data number) +(datamax= INDEF) Max data value / cosmic ray threshold +(fibers = 3) Number of fibers +(width = 6.) Width of profiles (pixels) +(crval = INDEF) Approximate wavelength +(cdelt = INDEF) Approximate dispersion +(objaps = 2) Object apertures +(arcaps = 1,3) Arc apertures + +(scatter= no) Subtract scattered light? +(fitflat= yes) Fit and ratio flat field spectrum? +(recente= yes) Recenter object apertures? +(edit = no) Edit/review object apertures? +(clean = no) Detect and replace bad pixels? +(dispcor= yes) Dispersion correct spectra? +(splot = yes) Plot the final spectrum? +(redo = no) Redo operations if previously done? +(update = yes) Update spectra if cal data changes? +(batch = no) Extract objects in batch? +(listonl= no) List steps but don't process? + +(params = ) Algorithm parameters + +.V2 +The input images are specified by image lists. The lists may be +a list of explicit, comma separate image names, @ files, or image +templates using pattern matching against file names in the directory. +The aperture reference spectrum is used to find the spectrum profiles and trace +them. Thus, this requires an image with good signal in all fibers +which usually means a flat field spectrum. It is recommended that +flat field correction be done using one dimensional extracted spectra +rather than as two dimensional images. This is done if a flat field +spectrum is specified. The arc assignment table is used to specifically +assign arc spectra to particular object spectra and the format +of the file is described in \fBrefspectra\fR. +.LP +The detector read out noise and gain are used for cleaning and variance +(optimal) extraction. +The variance +weighting and cosmic-ray cleanning are sensitive to extremely strong +cosmic-rays; ones which are hundreds of times brighter than the +spectrum. The \fIdatamax\fR is used to set an upper limit for any +real data. Any pixels above this value will be flagged as cosmic-rays +and will not affect the extractions. +The dispersion axis defines the wavelength direction +of spectra in the image if not defined in the image header by the keyword +DISPAXIS. The width parameter (in pixels) is used for the profile finding and +centering algorithm (\fBcenter1d\fR). +.LP +The number of fibers is fairly obvious. It is the number of +fibers, including the arc fibers, to be automatically found and +assigned apertures. The apertures are assigned aperture +numbers sequentially. The object and arc fibers are identified +by these aperture numbers as specified by the \f(CWobjaps\fR and +\f(CWarcaps\fR parameters. The defaults are for the case of three +fibers in the sequence arc fiber, object fiber, and arc fiber. +.LP +The approximate central wavelength and dispersion are used for the +automatic identification of the arc reference. They may be specified +as image header keywords or values. The INDEF values search the +entire range of the coordinate reference file but the automatic +line identification algorithm works much better and faster if +approximate values are given. +.LP +The next set of parameters select the processing steps and options. The +scattered light option allows fitting and subtracting a scattered light +surface from the input object and flat field. If there is significant +scattered light which is not subtracted the fiber throughput correction +will not be accurate. The +flat fitting option allows fitting and removing the overall shape of the +flat field spectra while preserving the pixel-to-pixel response +corrections. This is useful for maintaining the approximate object count +levels and not introducing the reciprocal of the flat field spectrum into +the object spectra. +.LP +The apertures defined for the aperture reference image are assigned to +each image. For the object images the apertures may be shifted across +the dispersion by recentering the strongest profiles and averaging +the individual shifts to form a single shift for all apertures. This +corrects for shifts in the detector during the observations. The +\f(CWrecenter\fR parameter selects whether to apply this shift or not. +.LP +The \f(CWedit\fR option allows you to be queried to review the apertures +assigned to each object image. If selected and the query answered +affirmatively the apertures may be interactively shifted and resized. The +query may also be answered with "NO" to turn off this option during +processing. Note that the initial aperture definitions for the aperture +reference image always allows editing. +.LP +The \f(CWclean\fR option invokes a profile fitting and deviant +point rejection algorithm as well as a variance weighting of points in the +aperture. These options require knowing the effective (i.e. accounting for +any image combining) read out noise and gain. For a discussion of cleaning +and variance weighted extraction see \fBapvariance\fR and +\fBapprofiles\fR. +.LP +The dispersion correction option selects whether to extract arc spectra, +determine dispersion functions, assign them to the object spectra, and, +possibly, resample the spectra to a linear (or log-linear) wavelength +scale. +.LP +The \f(CWsplot\fR option allows a query (which may be answered with "YES" +or "NO" to eliminate the query) and then plotting of the final object +spectra if answered affirmatively. The plotting is done with the +task \fBsplot\fR. +.LP +Generally once a spectrum has been processed it will not be reprocessed if +specified as an input spectrum. However, changes to the underlying +calibration data can cause such spectra to be reprocessed if the +\f(CWupdate\fR flag is set. The changes which will cause an update are a new +reference image, new flat field, and a new arc reference image. If all +input spectra are to be processed regardless of previous processing the +\f(CWredo\fR flag may be used. Note that reprocessing clobbers the +previously processed output spectra. +.LP +The \f(CWbatch\fR processing option allows object spectra to be processed as +a background or batch job. This will only occur if the aperture editing +and final spectrum plotting have been turned off, either with the task +option parameter or by answering "NO" to the queries. The \f(CWlistonly\fR +option prints a summary of the processing steps which will be performed on +the input spectra without actually doing anything. This is useful for +verifying which spectra will be affected if the input list contains +previously processed spectra. The listing does not include any arc spectra +which may be extracted to dispersion calibrate an object spectrum. +.LP +The last parameter (excluding the task mode parameter) points to another +parameter set for the algorithm parameters. The way \fBdo3fiber\fR works +this may not have any value and the parameter set \fBparams\fR is always +used. The algorithm parameters are discussed further in the next section. +.NH +Algorithms and Algorithm Parameters +.LP +This section summarizes the various algorithms used by the \fBdo3fiber\fR +task and the parameters which control and modify the algorithms. The +algorithm parameters available to the user are collected in the parameter +set \fBparams\fR. These parameters are taken from the various general +purpose tasks used by the \fBdo3fiber\fR processing task. Additional +information about these parameters and algorithms may be found in the help +for the actual task executed. These tasks are identified in the parameter +section listing in parenthesis. The aim of this parameter set organization +is to collect all the algorithm parameters in one place separate from the +processing parameters and include only those which are relevant for +this type of data. The parameter values can be changed from the +defaults by using the parameter editor, +.V1 + + cl> epar params + +.V2 +or simple typing \f(CWparams\fR. The parameter editor can also be +entered when editing the \fBdo3fiber\fR parameters by typing \f(CW:e +params\fR or simply \f(CW:e\fR if positioned at the \f(CWparams\fR +parameter. Figure 3 shows the parameter set. +.KS +.V1 + +.ce +Figure 3: Algorithm Parameter Set + + I R A F + Image Reduction and Analysis Facility +PACKAGE = kpnocoude + TASK = params + +(line = INDEF) Default dispersion line +(nsum = 10) Number of dispersion lines to sum +(extras = no) Extract sky, sigma, etc.? + + -- DEFAULT APERTURE LIMITS -- +(lower = -3.) Lower aperture limit relative to center +(upper = 3.) Upper aperture limit relative to center + + -- AUTOMATIC APERTURE RESIZING PARAMETERS -- +(ylevel = 0.05) Fraction of peak or intensity for resizing + +.KE +.KS +.V1 + -- TRACE PARAMETERS -- +(t_step = 10) Tracing step +(t_funct= spline3) Trace fitting function +(t_order= 2) Trace fitting function order +(t_niter= 1) Trace rejection iterations +(t_low = 3.) Trace lower rejection sigma +(t_high = 3.) Trace upper rejection sigma + +.KE +.KS +.V1 + -- SCATTERED LIGHT PARAMETERS -- +(buffer = 1.) Buffer distance from apertures +(apscat1= ) Fitting parameters across the dispersion +(apscat2= ) Fitting parameters along the dispersion + +.KE +.KS +.V1 + -- APERTURE EXTRACTION PARAMETERS -- +(weights= none) Extraction weights (none|variance) +(pfit = fit1d) Profile fitting algorithm (fit1d|fit2d) +(lsigma = 3.) Lower rejection threshold +(usigma = 3.) Upper rejection threshold +(nsubaps= 1) Number of subapertures + +.KE +.KS +.V1 + -- FLAT FIELD FUNCTION FITTING PARAMETERS -- +(f_inter= yes) Fit flat field interactively? +(f_funct= spline3) Fitting function +(f_order= 20) Fitting function order + +.KE +.KS +.V1 + -- ARC DISPERSION FUNCTION PARAMETERS -- +(coordli= linelists$idhenear.dat) Line list +(match = 10.) Line list matching limit in Angstroms +(fwidth = 3.5) Arc line widths in pixels +(cradius= 4.) Centering radius in pixels +(i_funct= legendre) Coordinate function +(i_order= 3) Order of dispersion function +(i_niter= 3) Rejection iterations +(i_low = 3.) Lower rejection sigma +(i_high = 3.) Upper rejection sigma +(refit = yes) Refit coordinate function when reidentifying? +(addfeat= no) Add features when reidentifying? + +.KE +.KS +.V1 + -- AUTOMATIC ARC ASSIGNMENT PARAMETERS -- +(select = interp) Selection method for reference spectra +(sort = jd) Sort key +(group = ljd) Group key +(time = no) Is sort key a time? +(timewra= 17.) Time wrap point for time sorting + +.KE +.KS +.V1 + -- DISPERSION CORRECTION PARAMETERS -- +(lineari= yes) Linearize (interpolate) spectra? +(log = no) Logarithmic wavelength scale? +(flux = yes) Conserve flux? + +.KE +.V2 +.NH 2 +Aperture Definitions +.LP +The first operation is to define the extraction apertures, which include +the aperture width and position dependence with wavelength, for the object +and arc fibers. This is done on a reference spectrum which is usually a +flat field taken through both fibers. Other spectra will inherit the +reference apertures and may apply a correction for any shift of the orders +across the dispersion. The reference apertures are defined only once +unless the \f(CWredo\fR option is set. +.LP +The selected number of fibers are found automatically by selecting the +highest peaks in a cut across the dispersion. Apertures are assigned with +a limits set by the \f(CWlower\fR and \f(CWupper\fR parameter and numbered +sequentially. A query is then given allowing the apertures to be reviewed +interactively. If answered affirmatively a cut across the orders is shown +with the apertures marked and an interactive aperture editing mode is +entered (see \fBapedit\fR). The main thing to be concerned about is that +the aperture numbers agree with the \f(CWobjaps\fR and \f(CWarcaps\fR +definitions. The aperture numbers may be changed with the 'i' or 'o' +keys. The apertures may also be resized from the default limits. +To exit the background and aperture editing steps type 'q'. +.LP +Next the positions of the fiber profiles at various points along the +dispersion are measured and a "trace function" is fit. The user is asked +whether to fit the trace function interactively. This is selected to +adjust the fitting parameters such as function type and order. When +interactively fitting a query is given for each aperture. After the first +aperture one may skip reviewing the other traces by responding with "NO". +Queries made by \fBdo3fiber\fR generally may be answered with either lower +case "yes" or "no" or with upper case "YES" or "NO". The upper case +responses apply to all further queries and so are used to eliminate further +queries of that kind. +.LP +The above steps are all performed using tasks from the \fBapextract\fR +package and parameters from the \fBparams\fR parameters. As a quick +summary, the dispersion direction of the spectra are determined from the +package \fBdispaxis\fR parameter if not defined in the image header. The default +line or column for finding the orders and the number of image lines or +columns to sum are set by the \f(CWline\fR and \f(CWnsum\fR parameters. A line +of INDEF (the default) selects the middle of the image. The automatic +finding algorithm is described for the task \fBapfind\fR and basically +finds the strongest peaks. The tracing is done as described in +\fBaptrace\fR and consists of stepping along the image using the specified +\f(CWt_step\fR parameter. The function fitting uses the \fBicfit\fR commands +with the other parameters from the tracing section. +.NH 2 +Extraction +.LP +The actual extraction of the spectra is done by summing across the fixed +width apertures at each point along the dispersion. The default is to +simply sum the pixels using partial pixels at the ends. There is an +option to weight the sum based on a Poisson noise model using the +\f(CWreadnoise\fR and \f(CWgain\fR detector parameters. Note that if the +\f(CWclean\fR option is selected the variance weighted extraction is used +regardless of the \f(CWweights\fR parameter. The sigma thresholds for +cleaning are also set in the \fBparams\fR parameters. +.LP +The cleaning and variance weighting options require knowing the effective +(i.e. accounting for any image combining) read out noise and gain. These +numbers need to be adjusted if the image has been processed such that the +intensity scale has a different origin (such as a background light +subtraction) or scaling (such as caused by unnormalized flat fielding). +For optimal extraction and cleaning to work it is recommended that the +\f(CWfitflat\fR option be used. For further discussion of cleaning and +variance weighted extraction see \fBapvariance\fR and \fBapprofiles\fR as +well as \fBapsum\fR. +.NH 2 +Scattered Light Subtraction +.LP +Scattered light may be subtracted from the input two dimensional image as +the first step. This is done using the algorithm described in +\fBapscatter\fR. This can be important if there is significant scattered +light since the flat field/throughput correction will otherwise be +incorrect. The algorithm consists of fitting a function to the data +outside the defined apertures by a specified \fIbuffer\fR at each line or +column across the dispersion. The function fitting parameters are the same +at each line. Because the fitted functions are independent at each line or +column a second set of one dimensional functions are fit parallel to the +dispersion using the evaluated fit values from the cross-dispersion step. +This produces a smooth scattered light surface which is finally subtracted +from the input image. Again the function fitting parameters are the +same at each line or column though they may be different than the parameters +used to fit across the dispersion. +.LP +The first time the task is run with a particular flat field (or aperture +reference image if no flat field is used) the scattered light fitting +parameters are set interactively using that image. The interactive step +selects a particular line or column upon which the fitting is done +interactively with the \fBicfit\fR commands. A query is first issued +which allows skipping this interactive stage. Note that the interactive +fitting is only for defining the fitting functions and orders. When +the graphical \fBicfit\fR fitting is exited (with 'q') there is a second prompt +allowing you to change the buffer distance (in the first cross-dispersion +stage) from the apertures, change the line/column, or finally quit. +.LP +The initial fitting parameters and the final set parameters are recorded +in the \fBapscat1\fR and \fBapscat2\fR hidden parameter sets. These +parameters are then used automatically for every subsequent image +which is scattered light corrected. +.LP +The scattered light subtraction modifies the input 2D images. To preserve +the original data a copy of the original image is made with the same +root name and the word "noscat" appended. The scattered light subtracted +images will have the header keyword "APSCATTE" which is how the task +avoids repeating the scattered light subtraction during any reprocessing. +However if the \fIredo\fR option is selected the scattered light subtraction +will also be redone by first restoring the "noscat" images to the original +input names. +.NH 2 +Flat Field Correction +.LP +Flat field corrections may be made during the basic CCD processing; i.e. +direct division by the two dimensional flat field observation. In that +case do not specify a flat field spectrum; use the null string "". The +\fBdo3fiber\fR task provides an alternative flat field response correction +based on division of the extracted object spectra by the extracted flat field +spectra. A discussion of the theory and merits of flat fielding directly +verses using the extracted spectra will not be made here. The +\fBdo3fiber\fR flat fielding algorithm is the \fIrecommended\fR method for +flat fielding since it works well and is not subject to the many problems +involved in two dimensional flat fielding. +.LP +The first step is extraction of the flat field spectrum, if specified, +using the reference apertures. Only one flat field is allowed so if +multiple flat fields are required the data must be reduced in groups. +If the \f(CWfitflat\fR +option is selected (the default) the extracted flat field spectra are +averaged together and a smooth function is fit. The default fitting +function and order are given by the parameters \f(CWf_function\fR and +\f(CWf_order\fR. If the parameter \f(CWf_interactive\fR is "yes" then the +fitting is done interactively using the \fBfit1d\fR task which uses the +\fBicfit\fR interactive fitting commands. +.LP +The fitted function is divided into the individual flat field spectra to +remove the basic shape of the spectrum while maintaining the relative +individual pixel responses and any fiber to fiber differences. This step +avoids introducing the flat field spectrum shape into the object spectra +and closely preserves the object counts. +.LP +The final step is to normalize the flat field spectra by the mean counts over +all the fibers. This normalization step is simply to preserve the average +counts of the extracted object and arc spectra after division by the +response spectra. +.NH 2 +Dispersion Correction +.LP +If dispersion correction is not selected, \f(CWdispcor\fR=no, then the object +spectra are simply extracted. If it is selected the arc spectra are used +to dispersion calibrate the object spectra. There are four steps involved; +determining the dispersion functions relating pixel position to wavelength, +assigning the appropriate dispersion function to a particular observation, +determining a zero point wavelength shift from the arc fibers to be applied +to the object fiber dispersion functions, and either storing the nonlinear +dispersion functions in the image headers or resampling the spectra to +evenly spaced pixels in wavelength. +.LP +The first arc spectrum in the arc list is used to define the reference +dispersion solution. It is extracted using the reference aperture +definitions. The interactive task \fBautoidentify\fR is used to +automatically define the dispersion function in one fiber. Whether or not +it is successful the user is presented with the interactive identification +graph. The automatic identifications can be reviewed and a new solution or +corrections to the automatic solution may be performed. The dispersion +functions for the other fibers are then determined automatically by +reference to the first fiber using the task \fBreidentify\fR. Except in +batch mode a query is given allowing the reidentified arc spectra to be +examined interactively with \fBidentify\fR. This would normally be done +only if the information about the reidentification printed on the terminal +indicates a problem such as a large increase in the RMS. This query may be +eliminated in the usual way. +.LP +The set of arc dispersion function parameters are from \fBidentify\fR and +\fBreidentify\fR. The parameters define a line list for use in +automatically assigning wavelengths to arc lines, a parameter controlling +the width of the centering window (which should match the base line +widths), the dispersion function type and order, parameters to exclude bad +lines from function fits, and parameters defining whether to refit the +dispersion function, as opposed to simply determining a zero point shift, +and the addition of new lines from the line list when reidentifying +additional arc spectra. The defaults should generally be adequate and the +dispersion function fitting parameters may be altered interactively. One +should consult the help for the two tasks for additional details of these +parameters and the operation of \fBidentify\fR. +.LP +If resampling of the spectra is selected by the parameter \f(CWlinearize\fR +all the arc dispersion functions are combined to provide a default +starting and ending wavelength and dispersion with the same number of +pixels is determined and the user is queried for any changes. This +linear dispersion system will be applied to all spectra so that all +the final processed object spectra will have the same dispersion +sampling. +.LP +Once the reference dispersion functions are defined other arc spectra are +extracted as they are assign to the object spectra. The assignment of +arcs is done either explicitly with an arc assignment table (parameter +\f(CWarctable\fR) or based on a header parameter such as a time. +The assignments are made by the task \fBrefspectra\fR. When two arcs are +assigned to an object spectrum an interpolation is done between the two +dispersion functions. This makes an approximate correction for steady +drifts in the dispersion. Because the arc fibers monitor any zero point +shifts in the dispersion functions, due to translation and rotation of the +detector, it is probably only necessary to have one or two arc spectra, one +at the beginning and/or one at the end of the night. +.LP +The tasks \fBsetjd\fR and \fBsetairmass\fR are automatically run on all +spectra. This computes and adds the header parameters for the Julian date +(JD), the local Julian day number (LJD), the universal time (UTMIDDLE), and +the air mass at the middle of the exposure. The default arc assignment is +to use the Julian date grouped by the local Julian day number. The +grouping allows multiple nights of data to be correctly assigned at the +same time. +.LP +When the object spectra are extracted so are the simultaneous arc spectra. +A zero point shift of the arc spectra relative to the dispersion solutions +of an assigned full arc observation is computed using \fBreidentify\fR. +The zero point shifts from the arc fibers are then +interpolated across the detector based on the positions of the arc +apertures to the positions of the object apertures. A linear interpolation +is used which accounts for a rotation of the detector as well as a +translation along the dispersion. The interpolated zero point wavelength +shifts are then added to the dispersion functions from the full arc +observation for the object fibers. Note that this does not assume that the +object and arc fiber dispersion functions are the same or have the same +wavelength origin, but only that the interpolated shifts in wavelength zero +point apply to all fibers. When there are two assigned full arc spectra +the above steps are done independently and the final pair of zero point +corrected dispersion functions for each object fiber are combined using the +assigned weights. Once the dispersion function correction is determined +from the extracted arc fiber spectra they are deleted leaving only the +object spectra. +.LP +The last step of dispersion correction is setting the dispersion +of the object spectra. There are two choices here. +If the \f(CWlinearize\fR parameter is not set the nonlinear dispersion +functions are stored in the image header. Other IRAF tasks interpret +this information when dispersion coordinates are needed for plotting +or analysis. This has the advantage of not requiring the spectra +to be interpolated and the disadvantage that the dispersion +information is only understood by IRAF tasks and cannot be readily +exported to other analysis software. +.LP +If the \f(CWlinearize\fR parameter is set then the spectra are resampled to a +linear dispersion relation either in wavelength or the log of the +wavelength. The linear dispersion parameters are those defined +previously for the arc reference image. +.LP +The linearization algorithm parameters allow selecting the interpolation +function type, whether to conserve flux per pixel by integrating across the +extent of the final pixel, and whether to linearize to equal linear or +logarithmic intervals. The latter may be appropriate for radial velocity +studies. The default is to use a fifth order polynomial for interpolation, +to conserve flux, and to not use logarithmic wavelength bins. These +parameters are described fully in the help for the task \fBdispcor\fR which +performs the correction. +.NH +References +.NH 2 +IRAF Introductory References +.LP +Work is underway on a new introductory guide to IRAF. Currently, the +work below is the primary introduction. +.IP +P. Shames and D. Tody, \fIA User's Introduction to the IRAF Command +Language\fR, Central Computer Services, NOAO, 1986. +.NH 2 +CCD Reductions +.IP +F. Valdes, \fIThe IRAF CCD Reduction Package -- CCDRED\fR, Central +Computer Services, NOAO, 1987. +.IP +F. Valdes, \fIUser's Guide to the CCDRED Package\fR, Central +Computer Services, NOAO, 1988. Also on-line as \f(CWhelp ccdred.guide\fR. +.IP +P. Massey, \fIA User's Guide to CCD Reductions with IRAF\fR, Central +Computer Services, NOAO, 1989. +.NH 2 +Aperture Extraction Package +.IP +F. Valdes, \fIThe IRAF APEXTRACT Package\fR, Central Computer Services, +NOAO, 1987 (out-of-date). +.NH 2 +Task Help References +.LP +Each task in the \fBspecred\fR packages and tasks used by \fBdofibers\fR have +help pages describing the parameters and task in some detail. To get +on-line help type +.V1 + +cl> help \fItaskname\fR + +.V2 +The output of this command can be piped to \fBlprint\fR to make a printed +copy. + +.V1 + apall - Extract 1D spectra (all parameters in one task) + apdefault - Set the default aperture parameters + apedit - Edit apertures interactively + apfind - Automatically find spectra and define apertures + aprecenter - Recenter apertures + apresize - Resize apertures + apsum - Extract 1D spectra + aptrace - Trace positions of spectra + + bplot - Batch plot of spectra with SPLOT + calibrate - Apply extinction and flux calibrations to spectra + continuum - Fit and normalize the continuum of multispec spectra + deredden - Apply interstellar extinction corrections + dispcor - Dispersion correct spectra + dopcor - Doppler correct spectra + identify - Identify arc lines and determine a dispersion function + msresp1d - Create fiber response spectra from flat field and sky spectra + refspectra - Assign reference spectra to observations + reidentify - Reidentify arc lines and determine new dispersion functions + sapertures - Set or change aperture header information + sarith - Spectrum arithmetic + scombine - Combine spectra + scopy - Copy spectra including aperture selection and format changes + sensfunc - Create sensitivity function + setairmass - Compute effective airmass and middle UT for an exposure + setjd - Compute and set Julian dates in images + slist - List spectrum headers + specplot - Stack and plot multiple spectra + splot - Plot and analyze spectra + standard - Identify standard stars to be used in sensitivity calc + + do3fiber - Process KPNO coude three fiber spectra + demos - Demonstrations and tests + + Additional help topics + + onedspec.package - Package parameters and general description of package + apextract.package - Package parameters and general description of package + approfiles - Profile determination algorithms + apvariance - Extractions, variance weighting, cleaning, and noise model + center1d - One dimensional centering algorithm + icfit - Interactive one dimensional curve fitting +.V2 +.SH +Appendix A: DO3FIBER Parameters +.LP +.nr PS 8 +.nr VS 10 +objects +.LS +List of object spectra to be processed. Previously processed spectra are +ignored unless the \f(CWredo\fR flag is set or the \f(CWupdate\fR flag is set and +dependent calibration data has changed. Extracted spectra are ignored. +.LE +apref = "" +.LS +Aperture reference spectrum. This spectrum is used to define the basic +extraction apertures and is typically a flat field spectrum. +.LE +flat = "" (optional) +.LS +Flat field spectrum. If specified the one dimensional flat field spectra +are extracted and used to make flat field corrections. +.LE +arcs = "" (at least one if dispersion correcting) +.LS +List of primary, all fiber arc spectra. These spectra are used to define +the dispersion functions for each fiber apart from a possible zero point +correction made with simultaneous arc calibration fibers in the object +spectra. One fiber from the first spectrum is used to mark lines and set +the dispersion function interactively and dispersion functions for all +other fibers and arc spectra are derived from it. +.LE +arctable = "" (optional) (refspectra) +.LS +Table defining arc spectra to be assigned to object +spectra (see \fBrefspectra\fR). If not specified an assignment based +on a header parameter, \f(CWparams.sort\fR, such as the observation time is made. +.LE + +readnoise = "RDNOISE" (apsum) +.LS +Read out noise in photons. This parameter defines the minimum noise +sigma. It is defined in terms of photons (or electrons) and scales +to the data values through the gain parameter. A image header keyword +(case insensitive) may be specified to get the value from the image. +.LE +gain = "GAIN" (apsum) +.LS +Detector gain or conversion factor between photons/electrons and +data values. It is specified as the number of photons per data value. +A image header keyword (case insensitive) may be specified to get the value +from the image. +.LE +datamax = INDEF (apsum.saturation) +.LS +The maximum data value which is not a cosmic ray. +When cleaning cosmic rays and/or using variance weighted extraction +very strong cosmic rays (pixel values much larger than the data) can +cause these operations to behave poorly. If a value other than INDEF +is specified then all data pixels in excess of this value will be +excluded and the algorithms will yield improved results. +This applies only to the object spectra and not the flat field or +arc spectra. For more +on this see the discussion of the saturation parameter in the +\fBapextract\fR package. +.LE +fibers = 3 (apfind) +.LS +Number of fibers. This number is used during the automatic definition of +the apertures from the aperture reference spectrum. +.LE +width = 6. (apedit) +.LS +Approximate base full width of the fiber profiles. This parameter is used +for the profile centering algorithm. +.LE +crval = INDEF, cdelt = INDEF (autoidentify) +.LS +These parameters specify an approximate central wavelength and dispersion. +They may be specified as numerical values, INDEF, or image header keyword +names whose values are to be used. If one or both of these parameters are +specified as INDEF the search for a solution will be slower and more likely +to fail. +.LE +objaps = "2", arcaps = "1,3" +.LS +List of object and arc aperture numbers. These are used to +identify arc apertures for wavelength calibration and object apertures +for the final results. +.LE + +scattered = no (apscatter) +.LS +Smooth and subtracted scattered light from the object and flat field +images. This operation consists of fitting independent smooth functions +across the dispersion using data outside the fiber apertures and then +smoothing the individual fits along the dispersion. The initial +flat field, or if none is given the aperture reference image, are +done interactively to allow setting the fitting parameters. All +subsequent subtractions use the same fitting parameters. +.LE +fitflat = yes (flat1d) +.LS +Fit the composite flat field spectrum by a smooth function and divide each +flat field spectrum by this function? This operation removes the average +spectral signature of the flat field lamp from the sensitivity correction to +avoid modifying the object fluxes. +.LE +recenter = yes (aprecenter) +.LS +Recenter reference apertures for each object spectrum? +.LE +edit = no (apedit) +.LS +Review aperture definitions for each object spectrum? Note that this does +not apply to the initial reference aperture which always allows +interactive review of the aperture definitions. +.LE +clean = no (apsum) +.LS +Detect and correct for bad pixels during extraction? This is the same +as the clean option in the \fBapextract\fR package. If yes this also +implies variance weighted extraction and requires reasonably good values +for the readout noise and gain. In addition the datamax parameters +can be useful. +.LE +dispcor = yes +.LS +Dispersion correct spectra? Depending on the \f(CWparams.linearize\fR +parameter this may either resample the spectra or insert a dispersion +function in the image header. +.LE +splot = yes +.LS +Plot the final spectra with the task \fBsplot\fR? +.LE +redo = no +.LS +Redo operations previously done? If no then previously processed spectra +in the objects list will not be processed (unless they need to be updated). +.LE +update = yes +.LS +Update processing of previously processed spectra if aperture, flat +field, or dispersion reference definitions are changed? +.LE +batch = no +.LS +Process spectra as a background or batch job provided there are no interactive +options (\f(CWedit\fR and \f(CWsplot\fR) selected. +.LE +listonly = no +.LS +List processing steps but don't process? +.LE + +params = "" (pset) +.LS +Name of parameter set containing additional processing parameters. The +default is parameter set \fBparams\fR. The parameter set may be examined +and modified in the usual ways (typically with "epar params" or ":e params" +from the parameter editor). Note that using a different parameter file +is not allowed. The parameters are described below. +.LE + +.ce +-- PACKAGE PARAMETERS + +Package parameters are those which generally apply to all task in the +package. This is also true of \fBdo3fiber\fR. + +observatory = "observatory" +.LS +Observatory at which the spectra were obtained if not specified in the +image header by the keyword OBSERVAT. For NOAO data the image headers +identify the observatory as "kpno" or "ctio" so this parameter is not used. +For data from other observatories this parameter may be used +as describe in \fBobservatory\fR. +.LE +interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc) +.LS +Spectrum interpolation type used when spectra are resampled. The choices are: + +.V1 + nearest - nearest neighbor + linear - linear + poly3 - 3rd order polynomial + poly5 - 5th order polynomial + spline3 - cubic spline + sinc - sinc function +.V2 +.LE +dispaxis = 2 +.LS +Default dispersion axis. The dispersion axis is 1 for dispersion +running along image lines and 2 for dispersion running along image +columns. If the image header parameter DISPAXIS is defined it has +precedence over this parameter. +.LE +database = "database" +.LS +Database (directory) used for storing aperture and dispersion information. +.LE +verbose = no +.LS +Print verbose information available with various tasks. +.LE +logfile = "logfile", plotfile = "" +.LS +Text and plot log files. If a filename is not specified then no log is +kept. The plot file contains IRAF graphics metacode which may be examined +in various ways such as with \fBgkimosaic\fR. +.LE +records = "" +.LS +Dummy parameter to be ignored. +.LE +version = "KPNOCOUDE: ..." +.LS +Version of the package. +.LE + +.ce +PARAMS PARAMETERS + +The following parameters are part of the \fBparams\fR parameter set and +define various algorithm parameters for \fBdo3fiber\fR. + +.ce +-- GENERAL PARAMETERS -- + +line = INDEF, nsum = 10 +.LS +The dispersion line (line or column perpendicular to the dispersion +axis) and number of adjacent lines (half before and half after unless +at the end of the image) used in finding, recentering, resizing, +editing, and tracing operations. A line of INDEF selects the middle of the +image along the dispersion axis. +.LE +extras = no (apsum) +.LS +Include extra information in the output spectra? When cleaning or using +variance weighting the cleaned and weighted spectra are recorded in the +first 2D plane of a 3D image, the raw, simple sum spectra are recorded in +the second plane, and the estimated sigmas are recorded in the third plane. +.LE + +.ce +-- DEFAULT APERTURE LIMITS -- + +lower = -3., upper = 3. (apdefault) +.LS +Default lower and upper aperture limits relative to the aperture center. +These limits are used when the apertures are first found and may be +resized automatically or interactively. +.LE + +.ce +-- AUTOMATIC APERTURE RESIZING PARAMETERS -- + +ylevel = 0.05 (apresize) +.LS +Data level at which to set aperture limits during automatic resizing. +It is a fraction of the peak relative to a local background. +.LE + +.ce +-- TRACE PARAMETERS -- + +t_step = 10 (aptrace) +.LS +Step along the dispersion axis between determination of the spectrum +positions. Note the \f(CWnsum\fR parameter is also used to enhance the +signal-to-noise at each step. +.LE +t_function = "spline3", t_order = 2 (aptrace) +.LS +Default trace fitting function and order. The fitting function types are +"chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and +"spline3" cubic spline. The order refers to the number of +terms in the polynomial functions or the number of spline pieces in the spline +functions. +.LE +t_niterate = 1, t_low = 3., t_high = 3. (aptrace) +.LS +Default number of rejection iterations and rejection sigma thresholds. +.LE + +.ce +-- SCATTERED LIGHT PARAMETERS -- + +buffer = 1. (apscatter) +.LS +Buffer distance from the aperture edges to be excluded in selecting the +scattered light pixels to be used. +.LE +apscat1 = "" (apscatter) +.LS +Fitting parameters across the dispersion. This references an additional +set of parameters for the ICFIT package. The default is the "apscat1" +parameter set. +.LE +apscat2 = "" (apscatter) +.LS +Fitting parameters along the dispersion. This references an additional +set of parameters for the ICFIT package. The default is the "apscat2" +parameter set. +.LE + +.ce +-- APERTURE EXTRACTION PARAMETERS -- + +weights = "none" (apsum) +.LS +Type of extraction weighting. Note that if the \f(CWclean\fR parameter is +set then the weights used are "variance" regardless of the weights +specified by this parameter. The choices are: + +"none" +.LS +The pixels are summed without weights except for partial pixels at the +ends. +.LE +"variance" +.LS +The extraction is weighted by the variance based on the data values +and a poisson/ccd model using the \f(CWgain\fR and \f(CWreadnoise\fR +parameters. +.LE +.LE +pfit = "fit1d" (apsum) (fit1d|fit2d) +.LS +Profile fitting algorithm for cleaning and variance weighted extractions. +The default is generally appropriate for most data but users +may try the other algorithm. See \fBapprofiles\fR for further information. +.LE +lsigma = 3., usigma = 3. (apsum) +.LS +Lower and upper rejection thresholds, given as a number of times the +estimated sigma of a pixel, for cleaning. +.LE +nsubaps = 1 (apsum) +.LS +During extraction it is possible to equally divide the apertures into +this number of subapertures. +.LE + +.ce +-- FLAT FIELD FUNCTION FITTING PARAMETERS -- + +f_interactive = yes (fit1d) +.LS +Fit the composite one dimensional flat field spectrum interactively? +This is used if \f(CWfitflat\fR is set and a two dimensional flat field +spectrum is specified. +.LE +f_function = "spline3", f_order = 20 (fit1d) +.LS +Function and order used to fit the composite one dimensional flat field +spectrum. The functions are "legendre", "chebyshev", "spline1", and +"spline3". The spline functions are linear and cubic splines with the +order specifying the number of pieces. +.LE + +.ce +-- ARC DISPERSION FUNCTION PARAMETERS -- + +threshold = 10. (autoidentify/identify/reidentify) +.LS +In order for a feature center to be determined the range of pixel intensities +around the feature must exceed this threshold. +.LE +coordlist = "linelists$idhenear.dat" (autoidentify/identify) +.LS +Arc line list consisting of an ordered list of wavelengths. +Some standard line lists are available in the directory "linelists$". +.LE +match = -3. (autoidentify/identify) +.LS +The maximum difference for a match between the dispersion function prediction +value and a wavelength in the coordinate list. +.LE +fwidth = 3.5 (autoidentify/identify) +.LS +Approximate full base width (in pixels) of arc lines. +.LE +cradius = 4. (reidentify) +.LS +Radius from previous position to reidentify arc line. +.LE +i_function = "legendre", i_order = 3 (autoidentify/identify) +.LS +The default function and order to be fit to the arc wavelengths as a +function of the pixel coordinate. The functions choices are "chebyshev", +"legendre", "spline1", or "spline3". +.LE +i_niterate = 3, i_low = 3.0, i_high = 3.0 (autoidentify/identify) +.LS +Number of rejection iterations and sigma thresholds for rejecting arc +lines from the dispersion function fits. +.LE +refit = yes (reidentify) +.LS +Refit the dispersion function? If yes and there is more than 1 line +and a dispersion function was defined in the arc reference then a new +dispersion function of the same type as in the reference image is fit +using the new pixel positions. Otherwise only a zero point shift is +determined for the revised fitted coordinates without changing the +form of the dispersion function. +.LE +addfeatures = no (reidentify) +.LS +Add new features from a line list during each reidentification? +This option can be used to compensate for lost features from the +reference solution. Care should be exercised that misidentified features +are not introduced. +.LE + +.ce +-- AUTOMATIC ARC ASSIGNMENT PARAMETERS -- + +select = "interp" (refspectra) +.LS +Selection method for assigning wavelength calibration spectra. +Note that an arc assignment table may be used to override the selection +method and explicitly assign arc spectra to object spectra. +The automatic selection methods are: + +average +.LS +Average two reference spectra without regard to any sort parameter. +If only one reference spectrum is specified then it is assigned with a +warning. If more than two reference spectra are specified then only the +first two are used and a warning is given. +This option is used to assign two reference spectra, with equal weights, +independent of any sorting parameter. +.LE +following +.LS +Select the nearest following spectrum in the reference list based on the +sorting parameter. If there is no following spectrum use the nearest preceding +spectrum. +.LE +interp +.LS +Interpolate between the preceding and following spectra in the reference +list based on the sorting parameter. If there is no preceding and following +spectrum use the nearest spectrum. The interpolation is weighted by the +relative distances of the sorting parameter. +.LE +match +.LS +Match each input spectrum with the reference spectrum list in order. +This overrides the reference aperture check. +.LE +nearest +.LS +Select the nearest spectrum in the reference list based on the sorting +parameter. +.LE +preceding +.LS +Select the nearest preceding spectrum in the reference list based on the +sorting parameter. If there is no preceding spectrum use the nearest following +spectrum. +.LE +.LE +sort = "jd", group = "ljd" (refspectra) +.LS +Image header keywords to be used as the sorting parameter for selection +based on order and to group spectra. +A null string, "", or the word "none" may be use to disable the sorting +or grouping parameters. +The sorting parameter +must be numeric but otherwise may be anything. The grouping parameter +may be a string or number and must simply be the same for all spectra within +the same group (say a single night). +Common sorting parameters are times or positions. +In \fBdo3fiber\fR the Julian date (JD) and the local Julian day number (LJD) +at the middle of the exposure are automatically computed from the universal +time at the beginning of the exposure and the exposure time. Also the +parameter UTMIDDLE is computed. +.LE +time = no, timewrap = 17. (refspectra) +.LS +Is the sorting parameter a 24 hour time? If so then the time origin +for the sorting is specified by the timewrap parameter. This time +should precede the first observation and follow the last observation +in a 24 hour cycle. +.LE + +.ce +-- DISPERSION CORRECTION PARAMETERS -- + +linearize = yes (dispcor) +.LS +Interpolate the spectra to a linear dispersion sampling? If yes the +spectra will be interpolated to a linear or log linear sampling +If no the nonlinear dispersion function(s) from the dispersion function +database are assigned to the input image world coordinate system +and the spectral data are not interpolated. +.LE +log = no (dispcor) +.LS +Use linear logarithmic wavelength coordinates? Linear logarithmic +wavelength coordinates have wavelength intervals which are constant +in the logarithm of the wavelength. +.LE +flux = yes (dispcor) +.LS +Conserve the total flux during interpolation? If \f(CWno\fR the output +spectrum is interpolated from the input spectrum at each output +wavelength coordinate. If \f(CWyes\fR the input spectrum is integrated +over the extent of each output pixel. This is slower than +simple interpolation. +.LE + +.ce +ENVIRONMENT PARAMETERS +.LP +The environment parameter \fIimtype\fR is used to determine the extension +of the images to be processed and created. This allows use with any +supported image extension. For STF images the extension has to be exact; +for example "d1h". |