From fa080de7afc95aa1c19a6e6fc0e0708ced2eadc4 Mon Sep 17 00:00:00 2001 From: Joseph Hunkeler Date: Wed, 8 Jul 2015 20:46:52 -0400 Subject: Initial commit --- noao/onedspec/doc/sys/revisions.v31.ms.bak | 307 +++++++++++++++++++++++++++++ 1 file changed, 307 insertions(+) create mode 100644 noao/onedspec/doc/sys/revisions.v31.ms.bak (limited to 'noao/onedspec/doc/sys/revisions.v31.ms.bak') diff --git a/noao/onedspec/doc/sys/revisions.v31.ms.bak b/noao/onedspec/doc/sys/revisions.v31.ms.bak new file mode 100644 index 00000000..1c7c3b31 --- /dev/null +++ b/noao/onedspec/doc/sys/revisions.v31.ms.bak @@ -0,0 +1,307 @@ +.nr PS 9 +.nr VS 11 +.RP +.ND +.TL +NOAO Spectroscopy Packages Revision Summary: IRAF Version 2.10.3 +.AU +Francisco Valdes +.AI +IRAF Group - Central Computer Services +.K2 +P.O. Box 26732, Tucson, Arizona 85726 +March 1993 +.AB +This paper summarizes the changes in Version 3.1 of the IRAF/NOAO +spectroscopy packages, \fBonedspec\fR, \fBlongslit\fR, \fBapextract\fR, +and those in \fBimred\fR. These changes are part of +part of IRAF Version 2.10.3. A list of the revisions is: + +.nf +\(bu A simplified \fIequispec\fR image header format +\(bu \fIEquispec\fR format allows a larger number of apertures in an image +\(bu Extensions to allow tasks to work on 3D images +\(bu New task \fBspecshift\fR for applying a zeropoint dispersion shift +\(bu Revised \fBsapertures\fR to edit spectrum coordinate parameters +\(bu Revised \fBdispcor\fR to easily apply multiple dispersion corrections +\(bu Revised \fBscombine\fR weighting and scaling options +\(bu Revised \fBscopy\fR to better handle bands in 3D images +\(bu Revised \fBcalibrate, dopcor\fR, and \fBspecshift\fR to work on 2D/3D images +\(bu New color graphics capabilities in \fBsplot, specplot, sensfunc\fR, and \fBidentify\fR +\(bu All spectral tasks use a common package dispersion axis parameter +\(bu A more complete suite of tasks in the \fBlongslit\fR package +\(bu A \fIdatamax\fR parameter in the \fBimred\fR reduction scripts for better cleaning +\(bu Revised the \fBimred\fR reduction scripts to abort on non-CCD processed data +\(bu Revised fiber reduction tasks to include a scattered light subtraction option +\(bu Revised \fBdoslit\fR to take the reference arc aperture from the first object +\(bu Bug fixes +.fi +.AE +.NH +Spectral Image Formats and Dispersion World Coordinate Systems +.LP +As with the original release of V2.10 IRAF, the primary changes in the +NOAO spectroscopy +software in V2.10.3 are in the area of spectral image formats and dispersion +world coordinate systems (WCS). A great deal was learned from experience +with the first release and the changes in this release attempt to +address problems encountered by users. The main revisions are: + +.in +4 +.nf +\(bu A new WCS format called \fIequispec\fR. +\(bu Extensions to allow use of 3D images with arbitrary dispersion axis. +\(bu Elimination of limits on the number of apertures in an image under certain conditions. +\(bu Improved tools for manipulating the spectral coordinate systems. +\(bu Bug fixes and solutions to problems found in the previous release. +.fi +.in - 4 + +In the previous version all images with multiple spectra used a coordinate +system called \fImultispec\fR. This type of WCS is complex and difficult +to manipulate by image header editting tools. Only the case of a single +linearized spectrum per image, sometimes called \fIonedspec\fR format, +provided a simple header format. However, the \fBapextract\fR package +used the \fImultispec\fR format even in the case of extracting a single +spectrum so to get to the simple format required use of \fBscopy\fR. +.LP +In many cases all the spectra in a multispectrum image have the same linear +dispersion function. The new \fIequispec\fR format uses a simple linear +coordinate system for the entire image. This format is produced by the +spectral software whenever possible. In addition to being simple and +compatible with the standard FITS coordinate representation, the +\fIequispec\fR format also avoids a limitation of the \fImultispec\fR WCS +on the number of spectra in a single image. This has specific application +to multifiber spectrographs with more than 250 fibers. +.LP +For multiple spectrum data in which the spectra have differing +dispersion functions (such as echelle orders) or when the spectra are +not linearized but use nonlinear dispersion functions, the \fImultispec\fR +format is still used. It is the most general WCS representation. +The difficulties with modifying this coordinate system, \fBhedit\fR +cannot be used, are addressed by enhancing the \fBsapertures\fR task +and by the new task \fBspecshift\fR which covers the common case of +modifying the dispersion zeropoint. +.LP +A feature of the spectral tasks which operate on one dimensional spectra +is that they can operate on two dimensional long slit spectra by +specifying a dispersion axis and a summing factor. This feature has +been extended to three dimensional spectra such as occur with +Fabry-Perot and multichannel radio synthesis instruments. The +dispersion axis may be along any axis as specified by the DISPAXIS +image header keyword or by the \fIdispaxis\fR package parameter. The +summing factor parameter \fInsum\fR is now a string which may have +one or two values to allow separate summing factors along two spatial +axes. Also, some additional tasks which previously did not support this +feature are \fBcalibrate\fR, \fBdopcor\fR, and \fBspecshift\fR. +.LP +The gory details of the spectral image formats and world coordinate +systems are laid out in the new help topic \fIspecwcs\fR (also +available in a postscript version in the IRAF network documentation +archive as iraf/docs/specwcs.ps.Z). +.LP +Some of the bug fixes and solutions to problems found in the previous +release concerning the image formats and WCS are a problem with the WCS +dimensionality (WCSDIM keyword) with 3D images and problems reading various +imported nonstandard formats. It is hoped that all such formats, including +previous IRAF spectral formats will all be allowed by the software in the +latest release. +.NH +DISPCOR +.LP +The previous versions of \fBdispcor\fR, the dispersion correction task, was +designed to prevent accidental repeated application; it is incorrect to +apply the dispersion function from the original data to a linearized +spectrum. However, it is valid to determine a new dispersion solution, say +from a dispersion calibrated arc, and apply that as a second correction. +\fBDispcor\fR would not use a new dispersion function, as specified by the +REFSPEC keywords, if the dispersion calibration flag was set. In order to +override this the user needed to manually change this flag to indicate the +spectrum was uncorrected. The problem was that it was difficult to do this +with \fImultispec\fR format spectra because the flag is part of the complex +WCS attribute strings. +.LP +\fBDispcor\fR was revised to use a different logic to prevent accidental +recalibration using an unintended dispersion function. The logic is as +follows. Previously \fBdispcor\fR would simply change the dispersion +calibration flag after correcting a spectrum while leaving the dispersion +function reference spectrum keywords alone as a record. The revised +\fBdispcor\fR keeps this useful record but moves this it to a new keyword +DCLOGn (where n is a sequential integer). Because the REFSPEC keyword is +removed after each application of \fBdispcor\fR it now takes an explicit +act by the user to assign another dispersion function to a spectrum and so +it is not possible to accidentally reapply the same dispersion function +twice. Thus this version will apply additional dispersion functions by +simply adding new REFSPEC keywords. If they are absent the task resamples +the spectra based on the current dispersion relation as was the case +before. +.LP +The new version can also tell whether the data was calibrated by the +previous version. In this case the check on the dispersion calibration +flag is still used so that during the transition users are still protected +against accidentally applying the same reference dispersion function +twice. The new task \fBsapertures\fR can now be used to change the +dispersion calibration flag to override this checking more easily than was +the case previously. +.NH +New Tasks +.LP +In this release there is only one completely new task and one task which +was significantly redesigned. The new task is \fBspecshift\fR. It is +relatively simple, it adds a zero point shift to the dispersion coordinates +of spectra. This was the most common request for manipulating the spectral +world coordinate system. In this regard there was a common confusion about +the distinction between shifting the coordinate system and shifting the +pixel data. Generally what people want is to apply a shift such that +features in the spectrum move to the desired wavelength. One thought is to +apply the tasks \fBimshift\fR or \fBshiftlines\fR. The surprise is that +this does not to work. The pixels are actually shifted in the image array, +but these tasks also apply the same shift to the coordinate system so that +features in the spectrum remain at the same wavelength. What is really +required is to leave the pixel data alone and shift only the coordinate +system. That is what \fBspecshift\fR does. +.LP +While one hopefully does not need to directly manipulate the image header +keywords describing the coordinate system or other aspects of the spectra, +instead using such tasks as \fBspecshift\fR, there always seem to be cases +where this is needed or desired. In the V2.10 release of the spectral +software this was difficult because the general \fImultispec\fR format was +the norm and it has information encoded in the complex WCS attribute +strings. As mentioned previously several changes have been made reduce the +complexity. Now \fIequispec\fR format will generally be the rule and this +format has keywords which are more easily manipulated with \fBhedit\fR and +\fBwcsedit\fR. However, the task \fBsapertures\fR was revised to provide +an editing cabability specifically for spectral images, in either +\fImultispec\fR or \fIequispec\fR format, with options to change various +parameters globally or aperture-by-aperture. +.NH +New Features +.LP +There were a number of miscellaneous minor revisions and bug fixes. One of +the major new capabilities available with V2.10.3 is support for color +graphics if the graphics device supports it. \fBXgterm\fR supports color +on X-window systems with color monitors. Several of the spectral tasks +were modified to use different colors for marks and overplots. These tasks +include \fBsplot\fR, \fBspecplot\fR, \fBidentify\fR, and \fBsensfunc\fR. +In the case of \fBsensfunc\fR the user controls the various color +assignments with a task parameter or \fBgtools\fR colon command while in +other cases the next available color is used. +.LP +There were several changes to \fBscombine\fR equivalent to those in +\fBimcombine\fR. The weighting, when selected, was changed from the square +root of the exposure time or spectrum statistics to the value with no +square root. This corresponds to the more commonly used variance +weighting. Other options were added to specify the scaling and weighting +factors. These allow specifying an image header keyword or a file +containing the scale or weighting factors. A new parameter, "nkeep" has +been added to allow controling the maximum number of pixels rejected by the +clipping algorithms. Previously it was possible to reject all pixels even +when some of the data was good though with a higher scatter than estimated; +i.e. all pixels might be greater than 3 sigma from the mean without being +cosmic rays or other bad values. Finally a parameter \fIsnoise\fR was +added to include a sensitivity or scale noise component to a Poisson noise +model. +.LP +In \fBsplot\fR the 'p' and 'u' keys which assign and modify the dispersion +coordinates now include options for applying a zero point shift or a +doppler shift in addition to defining an absolute wavelength for a feature +or starting and ending wavelengths. There are also bug fixes to the +equivalent width calculations, it did not handle flux calibrated data, and +the scroll keys '(' and ')'. +.LP +There were several changes to make it easier to deal with with three +dimensional \fImultispec\fR and \fIequispec\fR data; that is the additional +data from the "extras" option in the \fBapextract\fR tasks. One was to fix +problems associated with an incorrect WCSDIM keyword. This allows use of +image sections or \fBimcopy\fR for extracting specific bands and +apertures. Another was to add a "bands" parameter in \fBscopy/sarith\fR to +allow selection of bands. Also the "onedspec" output format in \fBscopy\fR +copies any selected bands to separate one dimensional images. +.LP +As mentioned earlier, many of the \fBonedspec\fR tasks have been extended +to work on 2D and 3D spatial spectra. Some tasks which now have this +capability in this version and not the previous one are \fBcalibrate\fR and +\fBdopcor\fR. \fBIdentify\fR and \fBredentify\fR were extended to operate +on 3D images. +.NH +LONGSLIT +.LP +With the applicablity of more \fBonedspec\fR tasks to long slit data +the \fBlongslit\fR package was modified to add many new tasks. +This required adding additional package parameters. One new task +to point out is \fBcalibrate\fR. This task is now the prefered one +to use for extinction and flux calibration of long slit spectra +rather than the obsolete \fBextinction\fR and \fBfluxcalib\fR. +The obsolete tasks are still present in this release. +.NH +APEXTRACT +.LP +The \fBapextract\fR package had a few, mostly transparent, changes. In +the previous version the output image header format was always \fImultispec\fR +even when there was a single spectrum, either because only one aperture +was defined or because the output format parameter was "onedspec". +In this release the default WCS format is the simpler \fIequispec\fR. +.LP +In the \fBonedspec\fR and \fBimred\fR spectral reduction packages there is +a dispersion axis package parameter which is used to defined the dispersion +axis for images without a DISPAXIS keyword. This applies to all tasks. +However, the \fBapextract\fR tasks had the dispersion axis defined by their +own task parameters resulting in some confusion. To make things consistent +the dispersion axis parameter in \fBapextract\fR has been moved from the +tasks to a package parameter. Now in the \fBimred\fR spectral reduction +packages, there is just one dispaxis parameter in the package parameters +which applies to all tasks in those packages, both those from +\fBonedspec\fR and those from \fBapextract\fR. +.LP +Some hidden algorithm parameters were adjusted so that the cleaning and +variance weighting options perform better in some problem cases without +requiring a great deal of knowledge about things to tweak. +.NH +IMRED Spectroscopic Reduction Tasks +.LP +The various spectroscopic reductions tasks, those beginning with "do", have +had some minor revisions and enhancements in addition to those which apply +to the individual tasks which make up these scripts. In the latter class +is the output WCS format is \fBequispec\fR except for the echelle tasks and +when dispersion linearization is not done. Related to this is that the +multifiber tasks can operate on data with more than 250 fibers which was a +limitation of the \fBmultispec\fR format. +.LP +The dispersion axis parameter in the reduction tasks and in the other tasks +in the \fBimred\fR spectroscopy packages, such as the \fBapextract\fR +tasks, is now solely a package parameter. +.LP +All the scripts now check the input spectra for the presence of the CCDPROC +keyword and abort if it is not found. This keyword indicates that the data +have been processed for basic CCD calibrations, though it does not check +the operations themselves. For data reduced using \fBccdproc\fR this +keyword will be present. If these tasks are used on data not processed by +\fBccdproc\fR then it is a simple matter to add this keyword with +\fBhedit\fR. Obviously, the purpose of this change is to avoid +inadvertently operating on raw data. +.LP +All the "do" tasks now have a parameter "datamax". This minimizes the +effects of very strong cosmic rays during the extraction of object spectra; +it does not apply to flat field or arc spectra. When there is a very large +difference between data pixel values and cosmic ray pixel values, +especially true for very weak spectra, the cosmic ray cleanning operation +does not always work well. If it is possible to specify a threshold value +between the maximum real data value and cosmic rays then the cosmic ray +cleanning can be significantly improved by immediately rejecting those +pixels above the threshold. Of course the user must be careful that real +data does not exceed this value since such data will be excluded. +.LP +The fiber reduction tasks, \fBdoargus, dohydra, dofibers, dofoe\fR, and +\fBdo3fiber\fR have a new processing option for subtracting scattered +light. This is particularly useful if there is significant scattered light +in producing uniform sky spectra for sky subtraction since the fiber +throughput calibration does not generally correct for this. +.LP +The slit reduction task \fBdoslit\fR previously required that the spectrum +for the reference arc cover the middle of the input data images. There +were cases of instrument configurations where this was not true requiring +additional manipulation to use this task. This requirement has been +eliminated. Instead when the reference arc needs to be extracted it uses +the aperture definition from one of the input object spectra since +definition of the object apertures occurs prior to setting up the +dispersion calibration. -- cgit