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diff --git a/noao/imred/echelle/doc/doecslit.ms b/noao/imred/echelle/doc/doecslit.ms new file mode 100644 index 00000000..a93f3e8b --- /dev/null +++ b/noao/imred/echelle/doc/doecslit.ms @@ -0,0 +1,1479 @@ +.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 Slit Spectra Reduction Task DOECSLIT +.AU +Francisco Valdes +.AI +IRAF Group - Central Computer Services +.K2 +.DY + +.AB +\fBDoecslit\fR subtracts background sky or scattered light, extracts, +wavelength calibrates, and flux calibrates multiorder echelle slit spectra +which have been processed to remove the detector characteristics; i.e. CCD +images have been bias, dark count, and flat field corrected. The spectra +should be oriented such that pixels of constant wavelength are aligned with +the image columns or lines. Small departures from this alignment are not +critical resulting in only a small loss of resolution. Single order +observations should be reduced with \fBdoslit\fR. +.AE +.NH +Introduction +.LP +\fBDoecslit\fR subtracts background sky or scattered light, extracts, +wavelength calibrates, and flux calibrates multiorder echelle slit spectra +which have been processed to remove the detector characteristics; i.e. CCD +images have been bias, dark count, and flat field corrected. The spectra +should be oriented such that pixels of constant wavelength are aligned with +the image columns or lines. Small departures from this alignment are not +critical resulting in only a small loss of resolution. Single order +observations should be reduced with \fBdoslit\fR. +.LP +The 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 and a degree of guidance, automation, and +record keeping. In the following description and in the parameter section +the various general tasks used are identified. Further +information about those tasks and their parameters may be found in their +documentation. \fBDoecslit\fR also simplifies and consolidates parameters +from those tasks and keeps track of previous processing to avoid +duplications. +.LP +The general organization of the task is to do the interactive setup steps, +such as the aperture definitions and reference dispersion function +determination, first using representative calibration data and then perform +the majority of the reductions automatically, 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 there are many variations possible. +.NH +Usage Outline +.LP +.IP [1] 6 +The images are first processed with \fBccdproc\fR for overscan, +zero level, dark count, and flat field corrections. +.IP [2] +Set the \fBdoecslit\fR parameters with \fBeparam\fR. Specify the object +images to be processed, an aperture reference image (usually a bright +star spectrum) to use in finding the orders and defining the +aperture parameters, one or more arc images, and one or more standard +star images. If there are many object, arc, or standard star images +you might prepare "@ files". Set the detector and data +specific parameters. Select the processing options desired. +Finally you might wish to review the \fBsparams\fR algorithm parameters +though the defaults are probably adequate. +.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 current execution and no further queries of that +type will be made. +.IP [4] +The specified number of orders (ranked by peak strength) in the aperture +reference image are located and default fixed width apertures are +assigned. If the resize option is set the apertures are resized by finding +the level which is 5% (the default) of the peak above local background. +You then have the option of entering the aperture editing loop to check the +aperture positions, sizes, and background fitting parameters. This is +highly recommended. Note that it is important that the aperture numbers be +sequential with the orders and if any orders are skipped the aperture +numbers should also skip. It is also important to verify the background +regions with the 'b' key. Usually you want any changes made to the +background definitions to apply to all apertures so use the 'a' key to +select all apertures before modifying the background parameters. To exit +the background mode and then to exit the review mode use 'q'. +.IP [5] +The order 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 examine the traced positions and adjust the fitting parameters. To exit +the interactive fitting type 'q'. Not all orders need be examined and the +"NO" response will quit the interactive fitting using the last defined +fitting parameters on the remaining traces. +.IP [6] +Apertures are now defined for all standard and object images. This is only +done if there are no previous aperture definitions for the image. The +aperture references previously defined are used as the initial set of +apertures for each image. The apertures are then recentered by an average +shift over all orders and resized if that option is selected. +The apertures may also be retraced and interactively examined +for each image if the tracing option is selected and quicklook mode is not. +.IP [7] +If scattered light subtraction is selected the scattered light parameters +are set using the aperture reference image and the task \fBapscatter\fR. +The purpose of this is to interactively define the aperture buffer distance +for the scattered light and the cross and parallel dispersion fitting +parameters. The fitting parameters are taken from and recorded in the +parameter sets \fBapscat1\fR and \fBapscat2\fR. All other scattered light +subtractions are done noninteractively with these parameters. Note that +the scattered light correction modifies the input images. Scattered light +subtraction is not done in quicklook mode. +.IP [8] +If dispersion correction is selected the first arc in the arc list is +extracted. The dispersion function is defined using the task +\fBecidentify\fR. Identify a few arc lines in a few orders with 'm' and 'o' +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 [9] +If the flux calibration option is selected the standard star spectra are +processed (if not done previously). The images are background subtracted, +extracted, and wavelength calibrated. The appropriate arc +calibration spectra are extracted and the dispersion function refit +using the arc reference spectrum as a starting point. The standard star +fluxes through the calibration bandpasses are compiled. You are queried +for the name of the standard star calibration data file. Because echelle +spectra are often at much higher dispersion than the calibration data +interpolated bandpasses may be defined with the bandpass parameters in +\fBsparams\fR and checked or modified interactively. +.IP +After all the standard stars are processed a sensitivity function is +determined using the interactive task \fBsensfunc\fR. Finally, the +standard star spectra are extinction corrected and flux calibrated +using the derived sensitivity function. +.IP [10] +The object spectra are now automatically background subtracted +(an alternative to scattered light subtraction), +extracted, wavelength calibrated, and flux calibrated. +.IP [11] +The option to examine the final spectra with \fBsplot\fR may be given. +To exit type 'q'. In quicklook mode the spectra are plotted +noninteractively with \fBspecplot\fR. +.IP [12] +The final spectra will have the same name as the original 2D images +with a ".ec" extension added. +.NH +Spectra and Data Files +.LP +The basic input consists of echelle slit object, standard star, and arc +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. +The raw CCD images must be +processed to remove overscan, bias, dark count, and flat field effects. +This is generally done using the \fBccdred\fR package. Flat fields which +are not contaminated by low counts between the apertures may be prepared +with the task \fBapflatten\fR (recommended) or \fBapnormalize\fR. Lines of +constant wavelength across the orders should be closely aligned with one of +the image axes. Sometimes the orders are aligned rather than the spectral +features. This will result in a small amount of resolution loss but is +often acceptable. In some cases one may correct for misalignment with the +\fBrotate\fR task. More complex geometric problems and observations of +extended objects should be handled by the \fBlongslit\fR package and single +order observations should be processed by \fBdoslit\fR. +.LP +The aperture reference spectrum is generally a bright star. The arc +spectra are comparison arc lamp observations (they must all be of the same +type). 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 task \fBrefspectra\fR. +.LP +The final reduced spectra are recorded in two or three dimensional IRAF +images. The images have the same name as the original images with an added +".ec" extension. Each line in the reduced image is a one dimensional +spectrum with associated aperture, order, and wavelength +information. When the \f(CWextras\fR parameter is set 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. The special task \fBscopy\fR may be used to extract +specific apertures or to change format to individual one dimensional +images. The task \fBscombine\fR is used to combine or merge orders into +a single spectrum. +.NH +Package Parameters +.LP +The \fBechelle\fR package parameters, shown in Figure 1, set parameters +which change infrequently and define the standard I/O functions. +.KS + +.ce +Figure 1: Package Parameter Set for the ECHELLE Package + +.V1 +cl> epar echelle + I R A F + Image Reduction and Analysis Facility +PACKAGE = imred + TASK = echelle + +(extinct= onedstds$kpnoextinct.dat) Extinction file +(caldir = onedstds$spechayescal/) 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) Text log file +(plotfil= ) Plot file + +(records= ) Record number extensions +(version= ECHELLE V3: July 1991) + +.KE +.V2 +The extinction file +is used for making extinction corrections and the standard star +calibration directory is used for determining flux calibrations from +standard star observations. The calibration directories contain data files +with standard star fluxes and band passes. The available extinction +files and flux calibration directories may be listed using the command: +.V1 + + cl> page onedstds$README + +.V2 +The extinction correction requires computation of an air mass using the +task \fBsetairmass\fR. The air mass computation needs information +about the observation and, in particular, the latitude of the observatory. +This is determined using the OBSERVAT image header keyword. If this +keyword is not present the observatory parameter is used. See the +task \fBobservatory\fR for more on defining the observatory parameters. +.LP +The spectrum interpolation type is used whenever a spectrum needs to be +resampled for linearization or performing operations between spectra +with different sampling. The "sinc" interpolation may be of interest +as an alternative but see the cautions given in \fBonedspec.package\fR. +.LP +The verbose parameter selects whether to print everything which goes +into the log file on the terminal. It is useful for monitoring +everything that the 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 the apertures, traces, and extracted +spectra but can become quite large. +.NH +Processing Parameters +.LP +The \fBdoecslit\fR parameters are shown in Figure 2. +.KS + +.ce +Figure 2: Parameter Set for DOECSLIT + +.V1 + I R A F + Image Reduction and Analysis Facility +PACKAGE = echelle + TASK = doecslit + +objects = List of object spectra +(apref = ) Aperture reference spectrum +(arcs = ) List of arc spectra +(arctabl= ) Arc assignment table (optional) +(standar= ) List of standard star spectra +.KE +.V1 + +(readnoi= 0.) Read out noise sigma (photons) +(gain = 1.) Photon gain (photons/data number) +(datamax= INDEF) Max data value / cosmic ray threshold +(norders= 10) Number of orders +(width = 5.) Width of profiles (pixels) + +(dispcor= yes) Dispersion correct spectra? +(extcor = no) Extinction correct spectra? +(fluxcal= no) Flux calibrate spectra? +(resize = no) Resize object apertures? +(clean = no) Detect and replace bad pixels? +(trace = yes) Trace object spectra? +(backgro= none) Background to subtract +(splot = no) Plot the final spectra? +(redo = no) Redo operations if previously done? +(update = no) Update spectra if cal data changes? +(quicklo= no) Approximate quicklook reductions? +(batch = no) Extract objects in batch? +(listonl= no) List steps but don't process? + +(sparams= ) 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. +To allow wildcard image lists to be used safely and conveniently the +image lists are checked to remove extracted images (the .ec images) +and to automatically identify object and arc spectra. Object and arc +images are identified by the keyword IMAGETYP with values of "object", +"OBJECT", "comp", or "COMPARISON" (the current practice at NOAO). +If arc images are found in the object list they are transferred to the +arc list while if object images are found in the arc list they are ignored. +All other image types, such as biases, darks, or flat fields, are +ignored. This behavior allows simply specifying all images with a wildcard +in the object list with automatic selections of arc spectra or a +wildcard in the arc list to automatically find the arc spectra. +If the data lack the identifying information it is up to the user +to explicitly set the proper lists. +.LP +As mentioned earlier, all the arc images must be of the same type; +that is taken with the same arc lamp. The aperture reference parameter +is a single image name which is usually a bright star. +.LP +The next set of parameters describe the noise characteristics and the +general layout of the orders. The read out noise and gain are used when +"cleaning" cosmic rays and when using variance or optimal weighting. These +parameters must be fairly accurate. Note that these are the effective +parameters and must be adjusted if previous processing has modified the +pixel values; such as with an unnormalized flat field. +.LP +The general direction in which the orders run is specified by the +dispersion axis parameter. Recall that ideally it is the direction +of constant wavelength which should be aligned with an image axis and +the dispersion direction will not be aligned because of the cross-dispersion. +The \f(CWnorders\fR parameter is used to automatically find the orders. The +specified number of the brightest peaks are found. Generally after finding the +orders the aperture definitions are reviewed and adjusted interactively. +The profile width should be approximately the full width at the profile +base. The default aperture limits and background regions are all +derived from this width parameter. +.LP +The next set of parameters select the processing steps and options. The +various calibration steps may be done simultaneously, that is at the same +time as the basic extractions, or in separate executions of the task. +Typically, all the desired operations are done at the same time. +Dispersion correction requires at least one arc spectrum and flux +calibration requires dispersion correction and at least one standard star +observation. +.LP +The \f(CWresize\fR option resets the edges of the extraction apertures based +on the profile for each object and standard star order. The default +resizing is to the 5% point relative to the peak measured above the +background. This allows following changes in the seeing. However, one +should consider the consequences of this if attempting to flux calibrate +the observations. Except in quicklook mode, the apertures for each object +and standard star observation may be reviewed graphically and further +adjustments made to the aperture width and background regions. +.LP +The apertures for each observation are adjusted for small shifts relative +to the reference aperture definitions. If you think this is not sufficient, +say to account for rotation of the detector or for differing atmospheric +dispersion, the \f(CWtrace\fR option allows redefining the aperture trace +functions for each observation. Note this is only allowed in non-quicklook +mode. +.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. See the next section for more about +requirements to use this option. +.LP +The \f(CWbackground\fR option selects a type of correction for background +or scattered light. If the type is "scattered" a global scattered light +is fit to the data between the apertures and subtracted from the images. +\fINote that the input images are modified by this operation\fR. +This option is slow and is not allowed in quicklook +mode. Alternatively, a local background may be subtracted using +background regions defined for each aperture. The background may be +within the slit for a sky subtraction or outside of the slit for a +local scattered light subtraction. The data in the regions +may be averaged, medianed, or the minimum value used. Another choice +is to fit the data in the background regions by a function and interpolate +to the object aperture. +.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, adding the scattered light subtraction option, a new arc +reference image, and new standard stars. 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 final step is to plot the spectra if the \f(CWsplot\fR option is +selected. In non-quicklook mode there is a query which may be +answered either in lower or upper case. The plotting uses the interactive +task \fBsplot\fR. In quicklook mode the plot appears noninteractively +using the task \fBspecplot\fR. +.LP +The \f(CWquicklook\fR option provides a simpler, less interactive, mode. +The quicklook mode automatically assigns the reference apertures to +the object and standard star observations without interactive review +or tracing, does not do the time consuming scattered light correction, +and the \f(CWsplot\fR option selects a noninteractive plot to be +shown at the end of processing of each object and standard star +spectrum. While the algorithms used in quicklook mode are nearly the same +as in non-quicklook mode and the final results may be the same it is +recommended that the greater degree of monitoring and review in +non-quicklook mode be used for careful final reductions. +.LP +The batch processing option allows object spectra to be processed as a +background or batch job. This will occur only if the interactive +\f(CWsplot\fR option is not active; either not set, turned off during +processing with "NO", or in quicklook mode. In batch processing the +terminal output is suppressed. +.LP +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 default +parameter set is called \fBsparams\fR. 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 +\fBdoecslit\fR task and the parameters which control and modify the +algorithms. The algorithm parameters available to you are +collected in the parameter set \fBsparams\fR. These parameters are +taken from the various general purpose tasks used by the \fBdoecslit\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 below. 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 echelle slit data. The parameter values +can be changed from the defaults by using the parameter editor, +.V1 + +cl> epar sparams + +.V2 +or simple typing \f(CWsparams\fR. +The parameter editor can also be entered when editing the \fBdoecslit\fR +parameters by typing \f(CW:e\fR when positioned at the \f(CWsparams\fR +parameter. Figure 3 shows the parameter set. +.KS + +.ce +Figure 3: Algorithm Parameter Set + +.V1 +cl> epar sparams + I R A F + Image Reduction and Analysis Facility +PACKAGE = echelle + TASK = sparams + +(line = INDEF) Default dispersion line +(nsum = 10) Number of dispersion lines to sum +(extras = no) Extract sky, sigma, etc.? + + -- AUTOMATIC APERTURE RESIZING PARAMETERS -- +(ylevel = 0.05) Fraction of peak or intensity for resizing +.KE +.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 + + -- BACKGROUND AND SCATTERED LIGHT PARAMETERS -- +(b_funct= legendre) Background function +(b_order= 1) Background function order +(b_naver= -100) Background average or median +(b_niter= 0) Background rejection iterations +(b_low = 3.) Background lower rejection sigma +(b_high = 3.) Background upper rejection sigma +(buffer = 1.) Buffer distance from apertures +(apscat1= ) Fitting parameters across the dispersion +(apscat2= ) Fitting parameters along the dispersion + + -- 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 + + -- ARC DISPERSION FUNCTION PARAMETERS -- +(coordli= linelist$thar.dat) Line list +(match = 1.) Line list matching limit in Angstroms +(fwidth = 4.) Arc line widths in pixels +(cradius= 10.) Centering radius in pixels +(i_funct= legendre) Echelle coordinate function +(i_xorde= 3) Order of coordinate function along dispersion +(i_yorde= 3) Order of coordinate function across dispersion +(i_niter= 3) Rejection iterations +(i_low = 3.) Lower rejection sigma +(i_high = 3.) Upper rejection sigma +(refit = yes) Refit coordinate function when reidentifying + + -- 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 + + -- DISPERSION CORRECTION PARAMETERS -- +(lineari= yes) Linearize (interpolate) spectra? +(log = no) Logarithmic wavelength scale? +(flux = yes) Conserve flux? + + -- SENSITIVITY CALIBRATION PARAMETERS -- +(bandwid= 10.) Bandpass widths +(bandsep= 10.) Bandpass separation +(s_inter= yes) Graphic interaction to examine/define bandpasses +(s_funct= spline3) Fitting function +(s_order= 1) Order of sensitivity function +(fnu = no) Create spectra having units of FNU? + +.V2 +.NH 2 +Aperture Definitions +.LP +The first operation is to define the extraction apertures, which include the +aperture width, background regions, and position dependence with +wavelength, for the input echelle slit spectra and, if flux calibration is +selected, the standard star spectra. This is done only for spectra which +do not have previously defined apertures unless the \f(CWredo\fR option is +set to force all definitions to be redone. Thus, apertures may be +defined separately using the \fBapextract\fR tasks. This is particularly +useful if one needs to use reference images to define apertures for very +weak spectra which are not well centered or traced by themselves. +.LP +Initially apertures are defined for a specified \fIaperture reference\fR +image. The selected number of orders are found automatically by selecting +the highest peaks in a cut across the dispersion. Apertures are assigned +with a width given by the \f(CWwidth\fR parameter and numbered sequentially. +The background regions are also defined in terms of the width parameter +starting at one width distance from the profile center and extending to two +widths on both sides of the profile. As an example, if the width parameter +is 5 pixels the default aperture limits are +/- 2.5 pixels and the +background sample regions will be "-10:-5,5:10". If the \f(CWresize\fR +parameter is set the aperture limits are adjusted to a specified point on +the spectrum profile (see \fBapresize\fR). +.LP +A query is then given allowing the aperture definitions to be reviewed and +modified. Queries made by \fBdoecslit\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 +Reviewing the aperture definitions is highly recommended to check the +aperture numbering, aperture limits, and background regions. The aperture +numbers must be linearly related, with a slope of +/- 1, to the true order +numbers though absolute order numbers need not be known. The key point is +that if an order is skipped the aperture numbers must also skip. The +background regions are checked with the 'b' key. Typically one adjusts all +the background regions at the same time by selecting all apertures with +the 'a' key first. To exit the background and aperture editing steps type +'q'. +.LP +Next the positions of the orders at various points along the dispersion +are measured and "trace functions" are fit. The user is asked whether +to fit each 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. +.LP +After the aperture reference image is done all the object and standard star +images are checked for aperture definitions and those without definitions +are assigned apertures. The assignment consists of inheriting the aperture +from the reference aperture image, recentering the apertures based on an +average shift that best centers all the apertures, resizing the apertures +if the resize option is selected, and retracing the spectral orders if the +retracing option is selected. Retracing is only allowed in non-quicklook +mode (set by the \f(CWquicklook\fR parameter). Also interactive review of +the aperture definitions is only done in +non-quicklook mode. In quicklook mode the aperture definitions are all set +noninteractively without retracing. It is recommended that quicklook only +be used for initial quick extractions and calibration and that for final +reductions one at least review the aperture definitions and possibly +retrace each observation. +.LP +The above steps are all performed using tasks from the \fBapextract\fR +package and parameters from the \fBsparams\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 object position on the slit 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 resizing is +described in the task \fBapresize\fR and the parameters used are also +described there. 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 +Background or Scattered Light Subtraction +.LP +In addition to not subtracting any sky or scattered light there are two +approaches to subtracting background light. The first is to determine +a smooth global scattered light component. The second is to subtract +a locally determined background at each point along the dispersion and +for each aperture. This can be either for a sky subtraction if the +background regions are within the slit or scattered light if the +background regions are outside of the slit. Note that background +subtraction is only done for object and standard star images and not +for arc spectra. Also, the global scattered light option is not done +in quicklook mode. +.LP +The global scattered light fitting and subtraction is done with the task +\fBapscatter\fR. The function fitting parameters are set interactively +using the aperture reference spectrum. All other subtractions are done +noninteractively with the same set of parameters. The scattered light is +subtracted from the input images, thus modifying them, and one might wish +to first make backups of the original images. +.LP +The scattered light is measured between the apertures using a specified +buffer distance from the aperture edges. The scattered light pixels are +fit by a series of one dimensional functions across the dispersion. The +independent fits are then smoothed along the dispersion by again fitting +low order functions. These fits then define the smooth scattered light +surface to be subtracted from the image. The fitting parameters are +defined and recorded in the two parameter sets \f(CWapscat1\fR and +\f(CWapscat2\fR. The scattered light algorithm is described more fully in +\fBapscatter\fR. This algorithm is relatively slow. +.LP +Local background subtraction is done during extraction based on background +regions and parameters defined by the default background parameters or +changed during interactive review of the apertures. The background +subtraction options are to subtract the average, median, or minimum of the +pixels in the background regions, or to fit a function and subtract the +function from under the extracted object pixels. The background regions +are specified in pixels from the aperture center and follow changes in +center of the spectrum along the dispersion. The syntax is colon separated +ranges with multiple ranges separated by a comma or space. The background +fitting uses the \fBicfit\fR routines which include medians, iterative +rejection of deviant points, and a choice of function types and orders. +Note that it is important to use a method which rejects cosmic rays such as +using either medians over all the background regions (\f(CWbackground\fR = +"median") or median samples during fitting (\f(CWb_naverage\fR < -1). The +background subtraction algorithm and options are described in greater +detail in \fBapsum\fR and \fBapbackground\fR. +.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 variance 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 \fBsparams\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 scattered light subtraction) or scaling (such as caused by unnormalized +flat fielding). These options also require using background subtraction +if the profile does not go to zero. For optimal extraction and +cleaning to work it is recommended that any flat fielding be done +using flat fields produced by \fBapflatten\fR, no scattered light +correction, and using background subtraction if there is any +appreciable sky or to compensate for scattered light. +For further discussion of cleaning and variance weighted extraction see +\fBapvariance\fR and \fBapprofiles\fR as well as \fBapsum\fR. +.NH 2 +Dispersion Correction +.LP +If dispersion correction is not selected, \f(CWdispcor\fR=no, then the object +spectra are simply extracted. The extracted spectra may be plotted +by setting the \f(CWsplot\fR option. This produces a query and uses +the interactive \fBsplot\fR task in non-quicklook mode and uses +\fBspecplot\fR noninteractively in quicklook mode. +.LP +Dispersion corrections are applied to the extracted spectra if the +\f(CWdispcor\fR processing parameter is set. There +are three basic steps involved; determining the dispersion functions +relating pixel position to wavelength, assigning the appropriate +dispersion function to a particular observation, and either storing +the nonlinear dispersion function 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 definition. +Note extractions of arc spectra are not background or scattered light +subtracted. The interactive task \fBecidentify\fR is used to define the +dispersion function. The idea is to mark some lines in a few orders whose +wavelengths are known (with the line list used to supply additional lines after +the first few identifications define the approximate wavelengths) and to fit a +function giving the wavelength from the aperture number and pixel position. +.LP +The arc dispersion function parameters are for \fBecidentify\fR and it's +related partner \fBecreidentify\fR. The parameters define a line list for +use in automatically assigning wavelengths to arc lines, a centering width +(which should match the line widths at the base of the lines), the +dispersion function type and orders, parameters to exclude bad lines from +function fits, and defining whether to refit the dispersion function as +opposed to simply determining a zero point shift. 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 interactive operation of +\fBecidentify\fR. +.LP +Once the reference dispersion function is defined other arc spectra are +extracted as required by 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. +This 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. +.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 +In non-quicklook mode the arc spectra assigned to each object are +extracted using the same apertures as the object. This accounts for +changes in the recentering, aperture sizes, and tracing functions. +In quicklook mode the arc spectra are extracted using the reference +apertures. When the same arc is used for several object images this +allows the arc spectrum to only be extracted once. +.LP +Defining the dispersion function for a new arc extraction is done with +the task \fBecreidentify\fR. This is done noninteractively with log +information recorded about the line reidentifications and the fit. +.LP +The last step of dispersion correction is setting the dispersion +of the object image from the arc images. There are two choices here. +If the \f(CWlinearize\fR parameter is not set the nonlinear dispersion +function is 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. For echelle spectra each order is linearized independently so +that the wavelength interval per pixel is different in different orders. +This preserves most of the resolution and avoids over or under sampling of +the highest or lowest dispersion orders. The wavelength limits are +taken from the limits determined from the arc reference spectrum and +the number of pixels is the same as the original images. The dispersion +per pixel is then derived from these constraints. +.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 2 +Flux Calibration +.LP +Flux calibration consists of an extinction correction and an instrumental +sensitivity calibration. The extinction correction only depends on the +extinction function defined by the package parameter \f(CWextinct\fR and +determination of the airmass from the header parameters (the air mass is +computed by \fBsetairmass\fR as mentioned earlier). The sensitivity +calibration depends on a sensitivity calibration spectrum determined from +standard star observations for which there are tabulated absolute fluxes. +The task that applies both the extinction correction and sensitivity +calibration to each extracted object spectrum is \fBcalibrate\fR. Consult +the manual page for this task for more information. +.LP +Generation of the sensitivity calibration spectrum is done before +processing any object spectra since it has two interactive steps and +requires all the standard star observations. The first step is tabulating +the observed fluxes over the same bandpasses as the calibrated absolute +fluxes. For very high resolution it may be the case that the measured +calibration bandpasses are too large or sparse. In this case one must +interpolate the calibration data to bandpasses appropriate for the data. +If the bandpass widths and separations are given as INDEF then the same +bandpasses as in the calibration file are used. Otherwise a uniform grid +of bandpasses is interpolated. Using interpolated bandpasses is not +rigorous but is sometimes the only choice for echelle spectra. +.LP +The standard star tabulations are done after each standard star is +extracted and dispersion corrected. You are asked for the name of the +standard star as tabulated in the absolute flux data files in the directory +\f(CWcaldir\fR defined by the package parameters. If the \f(CWinteract\fR +parameter is yes the bandpasses can be displayed on the data and you can +interactively add or delete bandpasses. The tabulation of the standard star +observations over the standard bandpasses is done by the task +\fBstandard\fR. The tabulated data is stored in the file \f(CWstd\fR. Note +that if the \f(CWredo\fR flag is not set any new standard stars specified in +subsequent executions of \fBdoecslit\fR are added to the previous data in +the data file, otherwise the file is first deleted. Modification of the +tabulated standard star data, such as by adding new stars, will cause any +spectra in the input list which have been previously calibrated to be +reprocessed if the \f(CWupdate\fR flag is set. +.LP +After the standard star calibration bandpass fluxes are tabulated the +information from all the standard stars is combined to produce a +sensitivity function for use by \fBcalibrate\fR. The sensitivity function +determination is interactive and uses the task \fBsensfunc\fR. This task +allows fitting a smooth sensitivity function to the ratio of the observed +to calibrated fluxes verses wavelength. The types of manipulations one +needs to do include deleting bad observations, possibly removing variable +extinction (for poor data), and possibly deriving a revised extinction +function. This is a complex operation and one should consult the manual +page for \fBsensfunc\fR. The sensitivity function is saved as one +dimensional spectra (one per order) with the root name \f(CWsens\fR. +Deletion of these images will also cause reprocessing to occur if the +\f(CWupdate\fR flag is set. +.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 and apidtable + apedit - Edit apertures interactively + apfind - Automatically find spectra and define apertures + apfit - Fit 2D spectra and output the fit, difference, or ratio + apflatten - Remove overall spectral and profile shapes from flat fields + apmask - Create and IRAF pixel list mask of the apertures +apnormalize - Normalize 2D apertures by 1D functions + aprecenter - Recenter apertures + apresize - Resize apertures + apscatter - Fit and subtract scattered light + apsum - Extract 1D spectra + aptrace - Trace positions of spectra + + bplot - Batch plots of spectra + calibrate - Apply extinction and flux calibrations to spectra + continuum - Fit the continuum in spectra + deredden - Apply interstellar extinction corrections + dispcor - Dispersion correct spectra + dopcor - Doppler correct spectra + ecidentify - Identify features in spectrum for dispersion solution +ecreidentify - Automatically identify features in spectra + refspectra - Assign wavelength reference spectra to other spectra + sarith - Spectrum arithmetic + scombine - Combine spectra + scopy - Select and copy apertures in different spectral formats + 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 header parameters + specplot - Stack and plot multiple spectra + splot - Preliminary spectral plot/analysis + standard - Identify standard stars to be used in sensitivity calc + + doecslit - Process Echelle slit 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: DOECSLIT Parameters +.LP +.nr PS 8 +.nr VS 10 +objects +.LS +List of object images 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. If the images contain the +keyword IMAGETYP then only those with a value of "object" or "OBJECT" +are used and those with a value of "comp" or "COMPARISON" are added +to the list of arcs. Extracted spectra are ignored. +.LE +apref = "" +.LS +Aperture reference spectrum. This spectrum is used to define the basic +extraction apertures and is typically a bright star spectrum. +.LE +arcs = "" (at least one if dispersion correcting) +.LS +List of arc calibration spectra. These spectra are used to define +the dispersion functions. The first spectrum is used to mark lines +and set the dispersion function interactively and dispersion functions +for all other arc spectra are derived from it. If the images contain +the keyword IMAGETYP then only those with a value of "comp" or +"COMPARISON" are used. All others are ignored as are extracted spectra. +.LE +arctable = "" (optional) (refspectra) +.LS +Table defining which arc spectra are to be assigned to which object +spectra (see \fBrefspectra\fR). If not specified an assignment based +on a header parameter, \f(CWsparams.sort\fR, such as the Julian date +is made. +.LE +standards = "" (at least one if flux calibrating) +.LS +List of standard star spectra. The standard stars must have entries in +the calibration database (package parameter \f(CWechelle.caldir\fR). +.LE + +readnoise = 0., gain = 1. (apsum) +.LS +Read out noise in photons and detector gain in photons per data value. +This parameter defines the minimum noise sigma and the conversion between +photon Poisson statistics and the data number statistics. Image header +keywords (case insensitive) may be specified to obtain the values from the +image header. +.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 standard star or +arc spectra. For more +on this see the discussion of the saturation parameter in the +\fBapextract\fR package. +.LE +norders = 10 (apfind) +.LS +Number of orders to be found automatically. +.LE +width = 5. (apedit) +.LS +Approximate full width of the spectrum profiles. This parameter is used +to define a width and error radius for the profile centering algorithm, +and defaults for the aperture limits and background regions. +.LE + +dispcor = yes +.LS +Dispersion correct spectra? This may involve either defining a nonlinear +dispersion coordinate system in the image header or resampling the +spectra to uniform linear wavelength coordinates as selected by +the parameter \f(CWsparams.linearize\fR. +.LE +extcor = no +.LS +Extinction correct the spectra? +.LE +fluxcal = no +.LS +Flux calibrate the spectra using standard star observations? +.LE +resize = no (apresize) +.LS +Resize the default apertures for each object based on the spectrum profile? +.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. In addition the datamax parameters +can be useful. +.LE +trace = yes (non-quicklook mode only) (aptrace) +.LS +Allow tracing each object spectrum separately? If not set then the trace +from the aperture reference is used, with recentering to allow for shifts +across the dispersion. If set then each object and standard star +image is retraced. Retracing is NOT done in quicklook mode. +.LE +background = "none" (apsum, apscatter) +.LS +Type of background light subtraction. The choices are "none" for no +background subtraction, "scattered" for a global scattered light +subtraction, "average" to average the background within background regions, +"median" to use the median in background regions, "minimum" to use the +minimum in background regions, or "fit" to fit across the dispersion using +the background within background regions. The scattered light option fits +and subtracts a smooth global background and modifies the input images. +This is a slow operation and so is NOT performed in quicklook mode. The +other background options are local to each aperture. The "fit" option uses +additional fitting parameters from \fBsparams\fR and the "scattered" option +uses parameters from \fBapscat1\fR and \fBapscat2\fR. +.LE +splot = no +.LS +Plot the final spectra? In quicklook mode a noninteractive, stacked plot +is automatically produced using the task \fBspecplot\fR while in +non-quicklook mode a query is given and the task \fBsplot\fR is used for +interactive plotting. +.LE +redo = no +.LS +Redo operations previously done? If no then previously processed spectra +in the objects list will not be processed unless required by the +update option. +.LE +update = no +.LS +Update processing of previously processed spectra if the aperture +reference image, the dispersion reference image, or standard star +calibration data are changed? +.LE +quicklook = no +.LS +Extract and calibrate spectra with minimal interaction? In quicklook mode +only aperture reference definitions, the initial dispersion function +solution, and the standard star setup are done interactively. Scattered +light subtraction and individual object tracing are not performed. +Normally the \f(CWsplot\fR option is set in this mode to produce an automatic +final spectrum plot for each object. It is recommended that this mode not be +used for final reductions. +.LE +batch = no +.LS +Process spectra as a background or batch job provided there are no interactive +steps remaining. +.LE +listonly = no +.LS +List processing steps but don't process? +.LE + +sparams = "" (pset) +.LS +Name of parameter set containing additional processing parameters. This +parameter is only for indicating the link to the parameter set +\fBsparams\fR and should not be given a value. The parameter set may be +examined and modified in the usual ways (typically with "epar sparams" +or ":e sparams" from the parameter editor). The parameters are +described below. +.LE + +.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 raw unweighted and uncleaned spectra, the background spectra, and +the estimated sigma spectra in a three dimensional output image format. +See the discussion in the \fBapextract\fR package for further information. +.LE + +.ce +-- AUTOMATIC APERTURE RESIZING PARAMETERS -- + +ylevel = 0.05 (apresize) +.LS +Fraction of the peak to set aperture limits during automatic resizing. +.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 +-- BACKGROUND AND SCATTERED LIGHT PARAMETERS -- + +b_function = "legendre", b_order = 1 (apsum) +.LS +Default background 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 +b_naverage = -100 (apsum) +.LS +Default number of points to average or median. Positive numbers +average that number of sequential points to form a fitting point. +Negative numbers median that number, in absolute value, of sequential +points. A value of 1 does no averaging and each data point is used in the +fit. +.LE +b_niterate = 0 (apsum) +.LS +Default number of rejection iterations. If greater than zero the fit is +used to detect deviant fitting points and reject them before repeating the +fit. The number of iterations of this process is given by this parameter. +.LE +b_low_reject = 3., b_high_reject = 3. (apsum) +.LS +Default background lower and upper rejection sigmas. If greater than zero +points deviating from the fit below and above the fit by more than this +number of times the sigma of the residuals are rejected before refitting. +.LE +buffer = 1. (apscatter) +.LS +Buffer distance from the edge of any aperture for data to be included +in the scattered light determination. This parameter may be modified +interactively. +.LE +apscat1 = "", apscat2 = "" (apscatter) +.LS +Parameter sets for the fitting functions across and along the dispersion. +These parameters are those used by \fBicfit\fR. These parameters are +usually set interactively. +.LE + +.ce +-- APERTURE EXTRACTION PARAMETERS -- + +weights = "none" (apsum) (none|variance) +.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 and approfile) (fit1d|fit2d) +.LS +Type of profile fitting algorithm to use. The "fit1d" algorithm is +preferred except in cases of extreme tilt. +.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 + +.ce +-- ARC DISPERSION FUNCTION PARAMETERS -- + +threshold = 10. (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 = "linelist$thar.dat" (ecidentify) +.LS +Arc line list consisting of an ordered list of wavelengths. +Some standard line lists are available in the directory "linelist$". +.LE +match = 1. (ecidentify) +.LS +The maximum difference for a match between the dispersion function computed +value and a wavelength in the coordinate list. +.LE +fwidth = 4. (ecidentify) +.LS +Approximate full base width (in pixels) of arc lines. +.LE +cradius = 10. (reidentify) +.LS +Radius from previous position to reidentify arc line. +.LE +i_function = "legendre", i_xorder = 3, i_yorder = 3 (ecidentify) +.LS +The default function, function order for the pixel position dependence, and +function order for the aperture number dependence to be fit to the arc +wavelengths. The functions choices are "chebyshev" or "legendre". +.LE +i_niterate = 3, i_low = 3.0, i_high = 3.0 (ecidentify) +.LS +Number of rejection iterations and sigma thresholds for rejecting arc +lines from the dispersion function fits. +.LE +refit = yes (ecreidentify) +.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 + +.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" (setjd and refspectra) +.LS +Image header keyword to be used as the sorting parameter for selection +based on order. The header parameter must be numeric but otherwise may +be anything. Common sorting parameters are times or positions. +.LE +group = "ljd" (setjd and refspectra) +.LS +Image header keyword to be used to group spectra. For those selection +methods which use the group parameter the reference and object +spectra must have identical values for this keyword. This can +be anything but it must be constant within a group. Common grouping +parameters are the date of observation "date-obs" (provided it does not +change over a night) or the local Julian day number. +.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 using +the linear dispersion parameters specified by other parameters. 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 is not interpolated. Note the interpolation +function type is set by the package parameter \f(CWinterp\fR. +.LE +log = no (ecdispcor) +.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 (ecdispcor) +.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 +-- SENSITIVITY CALIBRATION PARAMETERS -- + +bandwidth = 10., bandsep = 10. (standard) +.LS +Interpolated bandpass grid. If INDEF then the same bandpasses as in the +calibration files are used otherwise the calibration data is interpolated +to the specified set of bandpasses. +.LE +s_interact = yes (standard) +.LS +Display the bandpasses on the standard star data and allow interactive +addition and deletion of bandpasses. +.LE +s_function = "spline3", s_order = 1 (sensfunc) +.LS +Function and order used to fit the sensitivity data. The function types are +"chebyshev" polynomial, "legendre" polynomial, "spline3" cubic spline, +and "spline1" linear spline. +Order of the sensitivity fitting function. The value corresponds to the +number of polynomial terms or the number of spline pieces. The default +values may be changed interactively. +.LE +fnu = no (calibrate) +.LS +The default calibration is into units of F-lambda. If \f(CWfnu\fR = yes then +the calibrated spectrum will be in units of F-nu. +.LE + +.ce +PACKAGE PARAMETERS + +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. The default value defers to the +package parameter of the same name. +.LE +extinction = "onedstds$kpnoextinct.dat" (standard, sensfunc, calibrate) +.LS +Extinction file for a site. There are two extinction files in the +NOAO standards library, onedstds$, for KPNO and CTIO. These extinction +files are used for extinction and flux calibration. +.LE +caldir (standard) +.LS +Standard star calibration directory. A directory containing standard +star data files. Note that the directory name must end with '/'. +There are a number of standard star calibrations directories in the NOAO +standards library, onedstds$. +.LE +observatory = "observatory" (observatory) +.LS +The default observatory to use for latitude dependent computations. +If the OBSERVAT keyword in the image header it takes precedence over +this parameter. +.LE +interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc) (dispcor) +.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 +database = "database" +.LS +Database name used by various tasks. This is a directory which is created +if necessary. +.LE +verbose = no +.LS +Verbose output? If set then almost all the information written to the +logfile is also written to the terminal except when the task is a +background or batch process. +.LE +logfile = "logfile" +.LS +If specified detailed text log information is written to this file. +.LE +plotfile = "" +.LS +If specified metacode plots are recorded in this file for later review. +Since plot information can become large this should be used only if +really desired. +.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". |