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diff --git a/noao/onedspec/doc/sys/revisions.v3.ms b/noao/onedspec/doc/sys/revisions.v3.ms new file mode 100644 index 00000000..1c3da8be --- /dev/null +++ b/noao/onedspec/doc/sys/revisions.v3.ms @@ -0,0 +1,382 @@ +.nr PS 9 +.nr VS 11 +.RP +.ND +.TL +ONEDSPEC Package Revisions Summary: IRAF Version 2.10 +.AU +Francisco Valdes +.AI +IRAF Group - Central Computer Services +.K2 +P.O. Box 26732, Tucson, Arizona 85726 +July 1990 +.AB +This paper summarizes the changes in Version 3 of the IRAF \fBonedspec\fR +package which is part of IRAF Version 2.10. The major new features and +changes are: + +.IP \(bu +\fBIdentify\fR and \fBreidentify\fR now treat multispec format spectra +and two dimensional images as a unit. +.IP \(bu +\fBReidentify\fR supports both tracing (the old method) and always starting +with the primary reference vector when reidentifying other vectors in a +two dimensional reference image. +.IP \(bu +\fBReidentify\fR matches reference lines or apertures when reidentifying +those vectors in different images rather than tracing. +.IP \(bu +\fBReidentify\fR has an interactive capability to review +suspect reidentifications. +.IP \(bu +\fBReidentify\fR provides the capability to add new features. +.IP \(bu +The task \fBmsdispcor\fR provides for spatial interpolation of wavelength +zero point shifts from simultaneous arc spectra. +.IP \(bu +The new task \fBscopy\fR copies subsets of apertures and does format +conversions between the different spectrum formats. +.IP \(bu +The new task \fBsapertures\fR adds or modifies beam numbers and +aperture titles for selected apertures based on an aperture +identification file. +.IP \(bu +The new task \fBsfit\fR fits spectra and outputs the fits in various ways. +Apertures in multispec and echelle format are fit independently. +.IP \(bu +The task \fBcontinuum\fR now does independent fits for multispec and +echelle format spectra. +.IP \(bu +\fBSplot\fR now allows deblending of any number of components and +allows simultaneous fitting of a linear background. +.IP \(bu +The new task \fBfitprofs\fR fits 1D gaussian profiles in images. +.AE +.NH +Introduction +.PP +Though most of the ONEDSPEC package is unchanged there have been +significant changes to a number of the commonly used tasks in IRAF +Version 2.10. The changes will be made available as part of an +external package prior to the release of V2.10. This paper summarizes +the changes and new features. The changes primarily apply to multispec +or echelle format spectra. +.PP +Tables 1 and 2 summarize most of the major and minor changes in the package. + +.ce +TABLE 1: Summary of Major New Features and Changes + +.IP \(bu +\fBIdentify\fR and \fBreidentify\fR now treat multispec format spectra +and two dimensional images as a unit allowing easy movement between +different image lines or columns. The database is only updated upon +exiting the image. +.IP \(bu +\fBReidentify\fR supports both tracing (the old method) and always starting +with the primary reference vector when reidentifying other vectors in a +two dimensional reference image. +.IP \(bu +\fBReidentify\fR matches reference lines or apertures when reidentifying +those vectors in different images rather than tracing. +.IP \(bu +\fBReidentify\fR has an interactive capability to review +suspect reidentifications. +.IP \(bu +\fBReidentify\fR provides the capability to add new features. +.IP \(bu +The task \fBmsdispcor\fR allows using +auxilary reference spectra to provide a shift in the wavelength +zero point to the primary dispersion functions. This includes +spatial interpolation of simultaneous arc spectra in multifiber +spectrographs. +.IP \(bu +The new task \fBscopy\fR copies subsets of apertures and does format +conversions between the different spectrum formats. +.IP \(bu +The new task \fBsapertures\fR adds or modifies beam numbers and +aperture titles for selected apertures based on an aperture +identification file. +.IP \(bu +The new task \fBsfit\fR fits spectra and outputs the fits in various ways. +This includes a new feature to replace deviant points by the fit. +Apertures in multispec and echelle format are fit independently. +.IP \(bu +The task \fBcontinuum\fR now does independent fits for multispec and +echelle format spectra. +.IP \(bu +\fBSplot\fR now allows deblending of any number of components and +allows simultaneous fitting of a linear background. +.IP \(bu +The new task \fBfitprofs\fR fits 1D gaussian profiles to spectral lines or +features in an image line or column. This is done noniteractively and +driven by an input list of feature positions. +.bp +.LP +.ce +TABLE 2: Summary of Other New Features and Changes + +.IP \(bu +The \fBidentify\fR database format uses aperture numbers rather than +image sections for multispec format spectra. +.IP \(bu +The apertures in multispec format images need not be in the same order +or even the same number of apertures as the reference image in +\fBreidentify\fR or \fBmsdispcor\fR. +.IP \(bu +An automatic write parameter has been added to \fBidentify\fR. +.IP \(bu +The tasks \fBmsdispcor\fR and \fBspecplot\fR support the extra information +in the third dimension of multispec format spectra which is optionally +output by the \fBapextract\fR package. +.IP \(bu +\fBMsdispcor\fR and \fBspecplot\fR now include a logfile. +.IP \(bu +\fBSplot\fR selects spectra from multispec or echelle format by their +aperture number. Also a new keystroke was added to select a new +line/aperture without having to enter the image name again. +.IP \(bu +The task \fBspecplot\fR may select apertures from a multispec or +echelle format spectrum. +.IP \(bu +The aperture identification in multispec format is used, if present, +for labeling in \fBsplot\fR, \fBspecplot\fR, and \fBstandard\fR. +.NH +IDENTIFY and REIDENTIFY +.PP +These tasks have been modified for greater flexibility when dealing with +two dimensional images and multispec format spectra in particular. These +tasks were initially designed primarily to work on one dimensional images +with provisions for two dimensional images through image sections and +tracing to other parts of the image. Now these tasks treat such images +as a unit. +.PP +The task \fBidentify\fR has three added keystrokes, 'j', 'k', and 'o'. +These provide for moving between lines and columns of a two dimensional +image and different apertures in a multispec format spectrum. When +changing vectors the last set of features and fit are recalled, if they +have been previously defined, or the last set of features and fit are +inherited. For efficiency and to minimize queries, the feature +information from all the lines or apertures is not written to the +database until you quit the image (or explicitly write it) rather than +one at a time. A new parameter was also added, \fIautowrite\fR, which +may be set to automatically write the results to the database rather +than querying as is currently done. +.PP +The format of the database entries have also been slightly modified in +the case of multispec format images. Instead of using image sections +as part of the image name to define different vectors in the image +(this is still the case for regular two dimensional images) the aperture +number is recorded. This decouples the solutions for an aperture from +the specific image line allowing reference images to have a different +aperture order and additional or missing apertures. +.PP +While the changes to \fBidentify\fR are minor as far as usage, the task +\fBreidentify\fR is quite different and is essentially a new program. +Much of the complexity in this task relates to two dimensional images. +Two additions that apply to both one and two dimensional images is the +capability to add features from a coordinate list and to interactively +review the reidentifications using \fBidentify\fR. The addition of new +features may be useful in cases where the signal-to-noise varies or to +compensate for lost features when tracing across an image. The review +capability first prints the statistical results and then ask the user if +they want to examine the results interactively . This allows +basing the decision to interactively examine the features and fit based +on this information. Ideally, only a few of the worst cases need be +examined interactively. +.PP +There are two phases of reidentifications which apply to two +dimensional and multispec format images. In the first phase, one needs +to expand the identifications in the reference image from an initial, +interactively defined line, column, or aperture to other parts of the +reference image. A very important change is that there are now two +ways to transfer the features list; by successive steps (tracing) using +the previous results as a starting point (the only method provided in +the previous version) or always starting from the original reference +list. The first method is suitable for long slit spectra which have +significant positional trends across the image. If a feature is lost, +however, the feature remains missing (barring automatic addition as +mentioned above) for all following lines or columns. The latter method +is best if there are only small variations relative to the initial +reference or in multispec format spectra where there is no inherent +relation between apertures. +.PP +The second phase of reidentifications is between the reference image +and other images. In the previous version the primary reference vector +was transferred to the new image and then tracing would be applied +again. This compounds the problem with losing features during tracing +and prevents any possible reidentifications from multispec images in +which the wavelength range may vary greatly. In the new version there +is a direct reidentification from the same line, column, or aperture in +the reference to that of the next image. In the case where different +apertures may have significantly different wavelength coverage, as +occurs with aperture masks, it will at least be possible to +interactively identify features and coordinate functions for each +aperture, using the scrolling capability in the new \fBidentify\fR, in +just a single image and then correctly transfer the features to +additional images. +.PP +For multispec format spectra the database information is organized by +aperture number independent of image line number. Thus, it is possible +to reidentify features in multispec format spectra even if the aperture +order is different. If there is only a partial overlap in the aperture +set only those apertures having an entry in the reference image will be +done. +.NH +MSDISPCOR +.PP +The task \fBmsdispcor\fR dispersion corrects (rebins to a linear +dispersion function) multispec format spectra. It was introduced in +V2.8 of IRAF in the prototype \fBimred.msred\fR package. A number of +changes have been made in this task as summarized here. +.PP +The most fundamental change is support for spatial interpolation of +reference dispersion functions from a subset of apertures to other +apertures originating at different positions in a two dimensional +image. This is primarily intended for the case of comparison arc +spectra which are interspersed with object spectra in multifiber +spectrographs. It would also be useful in digitized photographic +spectra having calibration spectra exposed next to the object +spectrum. While usable directly, this feature is intended for the +processing scripts in the new \fBimred\fR fiber instrument packages. +.PP +The interpolation is only for a wavelength zero point shift, as determined +by \fBreidentify\fR with \fIrefit\fR=no. The full dispersion function +is still provided by a calibration image covering all apertures. Thus, +the simultaneous arc apertures are used to monitor shifts in the +detector relative to the full calibration which includes the relative +differences between each aperture and the arc monitoring apertures. +.PP +The multispec spectra containing the apertures used for the spatial +wavelength zero point corrections are specified in the image header +using the keywords REFSHFT1 and REFSHFT2. These are analogous to +the REFSPEC keywords used to define the reference dispersion functions +for the apertures. +.PP +As part of the general theme of multispec format support the +multispec dispersion reference spectra may have additional spectra and +need not be in the same order. However, all aperture in the +images being dispersion corrected must have dispersion relations +in the database. Multispec format spectra may include additional +data in the 3rd image dimension produced by the new +\fBapextract\fR package. \fBMsdispcor\fR rebins this information +in the same way as the spectra, thus, preserving the information +but now in linear wavelength sampling. +.PP +A new parameter, \fIlogfile\fR, has been added to capture information +about the dispersion correction process. +.NH +SCOPY and SAPERTURES +.PP +The task \fBscopy\fR is intended to bridge the gap between the various +spectrum formats and provide a tool to flexibly manipulate multispec +format spectra. It replaces the more primitve tasks +\fBmsred.msselect\fR and \fBechelle.ecselect\fR. Basically, this task +copies all or selected spectra from one format to a new image or images +of the same or different format. The typical uses are: + +.IP \(bu +Extract selected spectra from a multispec format image. +.IP \(bu +Allow converting the voluminous onedspec format from previous reductions +done before the multispec format was introduced into the more compact +multispec format. +.IP \(bu +Splice selected apertures from different multispec images into a new +multispec image. +.IP \(bu +Provide a quick way to convert lines or columns from two dimensional +long slit images into one dimensional spectra. This replaces +the task \fBproto.toonedspec\fR. +.PP +Because \fBscopy\fR can easily change the number and order of apertures +in the multispec image format it is important that the other tasks which +use the multispec format have been modified to be insensitive to which +line a spectrum is in and generally key off the aperture number. +.PP +The task \fBsapertures\fR is a simple way to set the aperture identifications, +APID keyword, and beam number, second field of APNUM keyword, based on +the aperture number and a simple text file. The text file contains lines +with aperture number, beam number, and (optional) title. This file is +used by the \fBapextract\fR package as well. Its likely usage is +to change image titles which might be wrong because of being inherited +from an aperture reference image during extraction. +.NH +SFIT, CONTINUUM, and ECCONTINUUM +.PP +The original version of \fBcontinuum\fR was a simple script based on +the task \fBfit1d\fR. The problem is that \fBfit1d\fR is intended to +process all the lines or columns in a two dimensional image +noninteractively. To do this it applies the same fitting parameters to +every line or column. The interactive step in this task is simply to +adjust fitting parameters. For spectra, particularly multispec and +echelle format spectra, one often needs to fit each spectrum +interactively and independently. When this problem was encountered for +the \fBechelle\fR package Rob Seaman wrote a nice program, +\fBeccontinuum\fR, which allows fitting a set of orders and keeps track +of which orders have been fit. +.PP +The general feature of the continuum fitting tasks is that they fit +spectra using the \fBicfit\fR interactive function fitting interface. +The results of the fit may be output as the fit itself, the difference +or residuals, the ratio, or the input data with rejected points replaced +by the fitted values. The last feature is new an provides a useful +spectrum cleaning option. The general equivalent to \fBfit1d\fR is +the new task \fBsfit\fR which provides the same independent fitting and +image line selection capabilites as \fBeccontinuum\fR. Note this task +is line oriented and does not select by aperture or order number. The +revised version of \fBcontinuum\fR is now based on \fBsfit\fR and +provides the independent continuum fitting capability for onedspec and +multispec format spectra that \fBeccontinuum\fR provides for echelle +format spectra. Technically what has been done is that \fBsfit\fR, +\fBcontinuum\fR, and \fBeccontinuum\fR are the same task; essentially +the task written by Seaman for echelle data. They differ in the +default parameters with the continuum fitting task having default +parameters providing continuum normalization (ratio) output and +iterative rejection values for excluding lines. +.NH +SPLOT, FITPROFS, and SPECPLOT +.PP +\fBSplot\fR has been modified to better support multispec and echelle +format images. The line selection for multispec and echelle format +spectra is now in terms of the aperture number rather than the image +line. The aperture title is used in place of the image title +if present. +.PP +The restriction to a maximum of four lines in the gaussian fitting and +deblending option of \fBsplot\fR has been lifted. Any number of +lines may be fit simultaneously, though execution time will become +long for a large number. In addition the fitting allows determining +a simultaneous linear background as well as using the cursor defined +points. The positions of the lines to be fit may be marked with +the cursor, typed in, or read from a file. The last choice is a new +feature. +.PP +In the past many people have used \fBsplot\fR for bulk, noninteractive +gaussian fitting by going through the trouble of redirecting the cursor +input, ukey input, text output, and graphics output. The main reason +this has been done is the lack of a one dimensional gaussian fitting +task. The task \fBfitprofs\fR has been added to provide simultaneous +gaussian fitting. This task takes a list of positions and optional +sigmas and fits gaussians to a list of images or spectra. The lines, +columns, or apertures may be selected. In addition a linear +background may be specified or included in the fitting. The output +consists of any combination of text similiar to the \fBsplot\fR +logfile, plots showing the data and fit, and image output of the fit or +the difference. This task is noninteractive; the interactive version +is the deblend command of \fBsplot\fR. The multiparameter, nonlinear +fitting software is the same as used in \fBsplot\fR. +.PP +\fBFitprofs\fR complements the task \fBstsdas.fitting.ngaussfit\fR from +the \fBstsdas\fR package (available from the Space Telescope Science +Institute). This task is similar in character to \fBfit1d\fR and has +an interactive one dimensional nonlinear function fitting interface +similar to \fBicfit\fR. +.PP +The task \fBspecplot\fR has a new parameter to select apertures to +plot. Previously there was no way to limit the apertures plotted other +than with image sections. All associated lines of a multispec +spectrum (those in the third dimension) are also plotted for the +selected apertures. This extra information is a new option of the +\fBapextract\fR package. |