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diff --git a/noao/onedspec/doc/sys/identify.ms b/noao/onedspec/doc/sys/identify.ms new file mode 100644 index 00000000..6a69204b --- /dev/null +++ b/noao/onedspec/doc/sys/identify.ms @@ -0,0 +1,347 @@ +.RP +.TL +Radial Velocity Measurements with IDENTIFY +.AU +Francisco Valdes +.AI +IRAF Group - Central Computer Services +.K2 +P.O. Box 26732, Tucson, Arizona 85726 +August 1986 +Revised August 1990 +.AB +The IRAF task \fBidentify\fP may be used to measure radial velocities. +This is done using the classical method of determining +the doppler shifted wavelengths of emission and absorption lines. +This paper covers many of the features and techniques available +through this powerful and versatile task which are not immediately +evident to a new user. +.AE +.sp 3 +.NH +\fBIntroduction\fP +.PP +The task \fBidentify\fP is very powerful and versatile. It can +be used to measure wavelengths and wavelength shifts for +doing radial velocity measurements from emission and +absorption lines. When combined with the CL's ability +to redirect input and output both from the standard text +streams and the cursor and graphics streams virtually +anything may be accomplished either interactively or +automatically. This, of course, requires quite a bit of +expertise and experience with \fBidentify\fP and with +the CL which a new user is not expected to be aware of initially. +This paper attempts to convey some of the possibilities. +There are many variations on these methods which the user +will learn through experience. +.PP +I want to make a caveat about the suggestions made in +this paper. I wrote the \fBidentify\fP task and so I am +an expert in its use. However, I am not a spectroscopist, +I have not been directly involved in the science of +measuring astronomical radial velocities, and I am not +very familiar with the literature. Thus, the suggestions +contained in this paper are based on my understanding of +the basic principles and the abilities of the \fBidentify\fP +task. +.PP +The task \fBidentify\fP is used to measure radial velocities +by determining the wavelengths of individual emission +and absorption lines. The user must compute the +radial velocities separately by relating the observed +wavelengths to the known rest wavelengths via the Doppler +formula. This is a good method when the lines are +strong, when there are only one or two features, and +when there are many, possibly, weaker lines. The +accuracy of this method is determined by the accuracy +of the line centering algorithm. +.PP +The alternative method is to compare an observed spectrum +to a template spectrum of known radial velocity. This +is done by correlation or fourier ratio methods. These +methods have the advantage of using all of the spectrum +and are good when there are many very weak and possibly +broad features. Their disadvantages are confusion +with telluric lines, they don't work well with just a +few real features, and they require a fair amount of +preliminary manipulation of the spectrum to remove +continuum and interpolate the spectrum in logarithmic +wavelength intervals. IRAF tasks for correlation +and fourier ratio methods are under development at +this time. Many people assume that these more abstract +methods are inherently better than the classical method. +This is not true, it depends on the quality and type of +data. +.PP +Wavelength measurements are best done on the original +data rather than after linearizing the wavelength +intervals. This is because 1) it is not necessary as +will be shown below and 2) the interpolation used to +linearize the wavelength scale can change the shape +of the lines, particularly strong, narrow emission +lines which are the best ones for determining radial +velocities. +.PP +This paper is specifically about \fBidentify\fP but one +should be aware of the task \fBsplot\fP which also may +be used to measure radial velocities. It differs in +several respects from \fBidentify\fP. \fBSplot\fP works +only on linearized data; the wavelength and pixel +coordinates are related by a zero point and wavelength +interval. The line centering algorithms are different; +the line centering is generally less robust (tolerant +of error) and often less accurate. It has many nice +features but is not designed for the specific purpose +of measuring positions of lines and, thus, is not as +easy to use for this purpose. +.PP +There are a number of sources of additional information +relating to the use of the task \fBidentify\fP. The +primary source is the manual pages for the task. As +with all manual pages it is available online with the +\fBhelp\fP command and in the \fIIRAF User Handbook\fP. +The NOAO reduction guides or cookbooks for the echelle +and IIDS/IRS include additional examples and discussion. +The line centering algorithm is the most critical +factor in determining dispersion solutions and radial +velocities. It is described in more detail under the +help topic \fBcenter1d\fP online or in the handbook. +.NH +Method 1 +.PP +In this method, arc calibration images are used to determine +a wavelength scale. The dispersion solution is then transferred +to the object spectrum and the wavelengths of emission and +absorption lines are measured and recorded. This is +relatively straightforward but some tricks will make this easier +and more accurate. +.NH 2 +Transferring Dispersion Solutions +.PP +There are several ways to transfer the dispersion solution +from an arc spectrum to an object spectrum differing in the +order in which things are done. +.IP (1) +One way is to determine the dispersion solution for all the arc images +first. To do this interactively specify all the arc images as the +input to \fBidentify\fP. After determining the dispersion solution for +the first arc and quitting (\fIq\fP key) the next arc will be displayed +with the previous dispersion solution and lines retained. Then use the +cursor commands \fIa\fP and \fIc\fP (all center) to recenter and +\fIf\fP (fit) to recompute the dispersion solution. If large shifts +are present use \fIs\fP (shift) or \fIx\fR (correlate peaks) to shift, +recenter, and compute a wavelength zero point shift to the dispersion +function. A new dispersion function should then be fit with \fIf\fP. +These commands are relatively fast and simple. +.IP +An important reason for doing all the arc images first +is that the same procedure can be done mostly noninteractively +with the task \fBreidentify\fP. After determining a +dispersion solution for one arc image \fBreidentify\fP +does the recenter (\fIa\fP and \fIc\fP), shift and +recenter (\fIs\fP), or correlation features, shift, and +recenter (\fIx\fP) to transfer the dispersion solutions +between arcs. This is usually done as a background task. +.IP +To transfer the solution to the object spectra specify +the list of object spectra as input to \fBidentify\fP. +For each image begin by entering the colon command +\fI:read arc\fP where arc is the name of the arc image +whose dispersion solution is to be applied; normally +the one taken at the same time and telescope position as +the object. This will read the dispersion solution and arc +line positions. Delete the arc line positions with the +\fIa\fP and \fId\fP (all delete) cursor keys. You +can now measure the wavelengths of lines in the spectrum. +.IP (2) +An alternative method is to interactively alternate between +arc and object spectra either in the input image list or +with the \fI:image name\fP colon command. +.NH 2 +Measuring Wavelengths +.IP (1) +To record the feature positions at any time use the \fI:features +file\fP colon command where \fIfile\fP is where the feature +information will be written. Repeating this with the same +file appends to the file. Writing to the database with the +\fI:write\fP colon command also records this information. +Without an argument the results are put in a file with +the same name as the image and a prefix of "id". You +can use any name you like, however, with \fI:write +name\fP. The \fI:features\fP command is probably preferable +because it only records the line information while the +database format includes the dispersion solution and +other information not needed for computing radial +velocities. +.IP (2) +Remember that when shifting between emission and absorption +lines the parameter \fIftype\fP must be changed. This may be done +interactively with the \fI:ftype emission\fP and \fI:ftype +absorption\fP commands. This parameter does not need to be +set except when changing between types of lines. +.IP (3) +Since the centering of the emission or absorption line is the +most critical factor, one should experiment with the parameter +\fIfwidth\fP. To change this parameter type \fI:fwidth value\fP. +The positions of the marked features are not changed until a +center command (\fIc\fP) command is given. +.IP +A narrow \fIfwidth\fP is less influenced by blends and wings but +has a larger uncertainty. A broad \fIfwidth\fP uses all of the +line profile and is thus stable but may be systematically influenced +by blending and wings. One possible approach is to measure +the positions at several values of \fIfwidth\fP and decide which +value to use or use some weighting of the various measurements. +You can record each set of measurements with the \fI:fe +file\fP command. +.IP (4) +For calibration of systematic effects from the centering one should +obtain the spectrum of a similar object with a known radial +velocity. The systematic effect is due to the fact that the +centering algorithm is measuring a weighted function of the +line profile which may not be the true center of the line as +tabulated in the laboratory or in a velocity standard. By +using the same centering method on an object with the same line +profiles and known velocity this effect can be eliminated. +.IP (5) +Since the arcs are not obtained at precisely the same time +as the object exposures, there may be a wavelength shift relative +to the arc dispersion solution. This may be calibrated from +night sky lines in the object itself (the night sky lines are +"good" in this case and should not be subtracted away). There are +generally not enough night sky lines to act as the primary +dispersion calibrator but just one can determine a possible +wavelength zero point shift. Measure the night sky line +positions at the same time the object lines are measured. +Determine a zero point shift from the night sky to be +taken out of the object lines. +.NH +Method 2 +.PP +This method is similar to the correlation method in that a +template spectrum is used and the average shift relative +to the template measures the radial velocity. This has the +advantage of not requiring the user to do a lot of calculations +(the averaging of the line shifts is done by identify) but is +otherwise no better than method 1. The template spectrum must +have the same features as the object spectrum. +.IP (1) +Determine a dispersion solution for the template spectrum +either from the lines in the spectrum or from an arc calibration. +.IP (2) +Mark the features to be correlated in the template spectrum. +.IP (3) +Transfer the template dispersion solution and line positions +to an object spectrum using one of the methods described +earlier. Then, for the current feature, point the cursor near +the same feature in the object spectrum and type \fIs\fP. The +mean shift in pixels, wavelength, and fractional wavelength (like +a radial velocity without the factor of the speed of light) +for the object is determined and printed. A new dispersion +solution is determined but you may ignore this. +.IP (4) +When doing additional object spectra, remember to start over +again with the template spectrum (using \fI:read template\fP) +and not the solution from the last object spectrum. +.IP (5) +This procedure assumes that the dispersion solution between +the template and object are the same. Checks for zero point +shifts with night sky lines, as discussed earlier, should be +made if possible. The systematic centering bias, however, is +accounted for by using the same lines from the template radial +velocity standard. +.IP (6) +One possible source of error is attempting to use very weak +lines. The recentering may find the wrong lines and affect +the results. The protections against this are the \fIthreshold\fP +parameter and setting the centering error radius to be relatively small. +.NH +Method 3 +.PP +This method uses only strong emission lines and works with +linearized data without an \fBidentify\fP dispersion +solution; though remember the caveats about rebinning the +spectra. The recipe involves measuring +the positions of emission lines. The +strongest emission lines may be found automatically using +the \fIy\fP cursor key. The number of emission lines to +be identified is set by the \fImaxfeatures\fP parameter. +The emission line positions are then written to a data file +using the \fI:features file\fP colon command. This may +be done interactively and takes only a few moments per +spectrum. If done interactively, the images may be chained +by specifying an image template. The only trick required +is that when proceeding to the next spectrum the previous +features are deleted using the cursor key combination \fIa\fP +and \fId\fP (all delete). +.PP +For a large number of images, on the order of hundreds, this +may be automated as follows. A file containing the cursor +commands is prepared. The cursor command format consists +of the x and y positions, the window (usually window 1), and +the key stroke or colon command. Because each new image from +an image template does not restart the cursor command file, +the commands would have to be repeated for each image in +the list. Thus, a CL loop calling the task each time with +only one image is preferable. Besides redirecting the +cursor input from a command file, we must also redirect the +standard input for the response to the database save query, the +standard output to discard the status line information, and , +possibly, the graphics to a metacode file which can then be +reviewed later. The following steps indicate what is to be +done. +.IP (1) +Prepare a file containing the images to be measured (one per line). +This can usually be done using the sections command to expand +a template and directing the output into a file. +.IP (2) +Prepare a cursor command file (let's call it cmdfile) +containing the following two lines. +.RS +.IP +.nf +.ft CW +1 1 1 y +1 1 1 :fe positions.dat +.ft P +.fi +.RE +.IP (3) +Enter the following commands. +.RS +.IP +.nf +.ft CW +list="file" +while (fscan (list,s1) !=EOF){ +print ("no") \(or identify (sl,maxfeatures=2, cursor="cmdfile", +>"dev$null", >G "plotfile") +} +.ft P +.fi +.RE +.LP +Note that these commands could be put in a CL script and executed +using the command +.sp +.IP +.ft CW +on> cl <script.cl +.ft P +.sp +.PP +The commands do the following. The first command initializes the +image list for the loop. The second command is the loop to +be run until the end of the image file is reached. The +command in the loop directs the string "no" to the standard +input of identify which will be the response to the database save +query. The identify command uses the image name obtained from the list +by the fscan procedure, sets the maximum number of features to be +found to be 2 (this can be set using \fBeparam\fP instead), the +cursor input is taken from the cursor command file, the standard +output is discarded to the null device, and the STDGRAPH output +is redirected to a plot file. If the plot file redirection is +not used, the graphs will appear on the specified graphics +device (usually the graphics terminal). The plot file can then +be disposed of using the \fBgkimosaic\fP task to either the +graphics terminal or a hardcopy device. |