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diff --git a/noao/onedspec/doc/onedspec.hlp b/noao/onedspec/doc/onedspec.hlp new file mode 100644 index 00000000..a1c06ab9 --- /dev/null +++ b/noao/onedspec/doc/onedspec.hlp @@ -0,0 +1,293 @@ +.help package Nov94 noao.onedspec +.ih +NAME +onedspec -- generic 1D spectral reduction and analysis package +.ih +USAGE +onedspec +.ih +PARAMETERS +.ls observatory = "observatory" +Observatory at which the spectra were obtained if not specified in the +image header by the keyword OBSERVAT. This parameter is used by several +tasks in the package through parameter redirection so this parameter may be +used to affect all these tasks at the same time. The observatory may be +one of the observatories in the observatory database, "observatory" to +select the observatory defined by the environment variable "observatory" or +the parameter \fBobservatory.observatory\fR, or "obspars" to select the +current parameters set in the \fBobservatory\fR task. See help for +\fBobservatory\fR for additional information. +.le +.ls caldir = "" +Calibration directory containing standard star data. This parameter +is used by several tasks in the package through redirection. A list of +standard calibration directories may be obtained by listing the file +"onedstds$README"; for example: + + cl> page onedstds$README + +The user may copy or create their own calibration files and specify +the directory. The directory "" refers to the current working directory. +.le +.ls interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc) +Spectrum interpolation type used when spectra are resampled. The choices are: + +.nf + nearest - nearest neighbor + linear - linear + poly3 - 3rd order polynomial + poly5 - 5th order polynomial + spline3 - cubic spline + sinc - sinc function +.fi +.le + +The following parameters apply to two and three dimensional images +such as long slit or Fabry-Perot spectra. They allow selection of +a line or column as the spectrum "aperture" and summing of neighboring +elements to form a one dimensional spectrum as the tasks in the +ONEDSPEC package expect. + +.ls dispaxis = 1 +The image axis corresponding to the dispersion. If there is an image +header keyword DISPAXIS then the value of the keyword will be used +otherwise this package parameter is used. The dispersion coordinates +are a function of column, line, or band when this parameter is 1, 2 +or 3. +.le +.ls nsum = "1" +The number of neighboring elements to sum. This is a string parameter +that can have one or two numbers. For two dimensional images only +one number is needed and specifies the number of lines or columns +to sum depending on the dispersion axis. For three dimensional +images two numbers may be given (if only one is given it defaults +to the same value for both spatial axes) to specify the summing of +the two spatial axes. The order is the lower dimensional spatial +axis first. + +For an even value the elements summed are the central specified +"aperture", nsum / 2 - 1 below, and nsum /2 above; i.e the +central value is closer to the lower element than the upper. +For example, for nsum=4 and an aperture of 10 for a dispersion +axis of 1 in a two dimensional image the spectrum used will be +the sum of lines 9 to 12. +.le + +.ls records = "" +This is a dummy parameter. It is applicable only in the \fBimred.irs\fR +and \fBimred.iids\fR packages. +.le +.ls version = "ONEDSPEC V3: November 1991" +Package version identification. +.le +.ih +DESCRIPTION +The \fBonedspec\fR package contains generic tasks for the reduction, +analysis, and display of one dimensional spectra. The specifics of +individual tasks may be found in their IRAF "help" pages. This document +describes the general and common features of the tasks. + +The functions provided in the \fBonedspec\fR package with applicable tasks +are summarized in Table 1. + +.ce +Table 1: Functions provided in the \fBonedspec\fR package + +.nf +1. Graphical display of spectra + bplot - Batch plots of spectra + identify - Identify features and fit dispersion functions + specplot - Stack and plot multiple spectra + splot - Interactive spectral plot/analysis + +2. Determining and applying dispersion calibrations + dispcor - Dispersion correct spectra + dopcor - Apply doppler corrections + identify - Identify features and fit dispersion functions + refspectra - Assign reference spectra to other spectra + reidentify - Automatically identify features in spectra + specshift - Shift spectral dispersion coordinate system + +3. Determining and applying flux calibrations + calibrate - Apply extinction and flux calibrations to spectra + deredden - Apply interstellar extinction correction + dopcor - Apply doppler corrections + lcalib - List calibration file data + sensfunc - Create sensitivity function + standard - Tabulate standard star data + +4. Fitting spectral features and continua + continuum - Fit the continuum in spectra + fitprofs - Fit gaussian profiles + sfit - Fit spectra and output fit, ratio, or difference + splot - Interactive spectral plot/analysis + +5. Arithmetic and combining of spectra + sarith - Spectrum arithmetic + scombine - Combine spectra + splot - Interactive spectral plot/analysis + +6. Miscellaneous functions + mkspec - Generate an artificial spectrum + names - Generate a list of image names from a string + sapertures - Set or change aperture header information + scopy - Select and copy spectra + sinterp - Interpolate a table of x,y to create a spectrum + slist - List spectrum header parameters + splot - Interactive spectral plot/analysis +.fi + +There are other packages which provide additional functions or specialized +tasks for spectra. Radial velocity measurements are available in the +\fBnoao.rv\fR package. The \fBnoao.imred\fR package contains a number +of packages for specific types of data or instruments. These packages +are listed in Table 2. + +.ce +Table 2: \fBImred\fR spectroscopy packages + +.nf + argus - CTIO ARGUS reduction package + ctioslit - CTIO spectrophotometric reduction package + echelle - Echelle spectral reductions (slit and FOE) + hydra - KPNO HYDRA (and NESSIE) reduction package + iids - KPNO IIDS spectral reductions + irs - KPNO IRS spectral reductions + kpnocoude - KPNO coude reduction package (slit and 3 fiber) + kpnoslit - KPNO low/moderate dispersion slits (Goldcam, RCspec, Whitecam) + specred - Generic slit and fiber spectral reduction package +.fi + +Finally, there are non-NOAO packages which may contain generally useful +software for spectra. Currently available packages are \fBstsdas\fR +and \fBxray\fR. +.ih +SPECTRUM IMAGE FORMATS AND COORDINATE SYSTEMS +See the separate help topic \fIspecwcs\fR. +.ih +INTERPOLATION +Changing the dispersion sampling of spectra, such as when converting to a +constant sampling interval per pixel or a common sampling for combining or +doing arithmetic on spectra, requires interpolation. The tasks which +reinterpolate spectra, if needed, are \fBdispcor, sarith, scombine,\fR and +\fBsplot\fR. + +The interpolation type is set by the package parameter \fIinterp\fR. +The available interpolation types are: + +.nf + nearest - nearest neighbor + linear - linear + poly3 - 3rd order polynomial + poly5 - 5th order polynomial + spline3 - cubic spline + sinc - sinc function +.fi + +The default interpolation type is a 5th order polynomial. + +The choice of interpolation type depends on the type of data, smooth +verses strong, sharp, undersampled features, and the requirements of +the user. The "nearest" and "linear" interpolation are somewhat +crude and simple but they avoid "ringing" near sharp features. The +polynomial interpolations are smoother but have noticible ringing +near sharp features. They are, unlike the sinc function described +below, localized. + +In V2.10 a "sinc" interpolation option is available. This function +has advantages and disadvantages. It is important to realize that +there are disadvantages! Sinc interpolation approximates applying a phase +shift to the fourier transform of the spectrum. Thus, repeated +interpolations do not accumulate errors (or nearly so) and, in particular, +a forward and reverse interpolation will recover the original spectrum +much more closely than other interpolation types. However, for +undersampled, strong features, such as cosmic rays or narrow emission or +absorption lines, the ringing can be more severe than the polynomial +interpolations. The ringing is especially a concern because it extends +a long way from the feature causing the ringing; 30 pixels with the +truncated algorithm used. Note that it is not the truncation of the +interpolation function which is at fault! + +Because of the problems seen with sinc interpolation it should be used with +care. Specifically, if there are no undersampled, narrow features it is a +good choice but when there are such features the contamination of the +spectrum by ringing is much more severe than with other interpolation +types. +.ih +UNITS +In versions of the NOAO spectroscopy packages prior to V2.10 the dispersion +units used were restricted to Angstroms. In V2.10 the first, +experimental, step of generalizing to other units was taken by +allowing the two principle spectral plotting tasks, \fBsplot\fR and +\fBspecplot\fR, to plot in various units. Dispersion functions are still +assumed to be in Angstroms but in the future the generalization will be +completed to all the NOAO spectroscopy tasks. + +The dispersion units capability of the plotting tasks allows specifying +the units with the "units" task parameter and interactively changing the +units with the ":units" command. In addition the 'v' key allows plotting +in velocity units with the zero point velocity defined by the cursor +position. + +The units are specified by strings having a unit type from the list below +along with the possible preceding modifiers, "inverse", to select the +inverse of the unit and "log" to select logarithmic units. For example "log +angstroms" to plot the logarithm of wavelength in Angstroms and "inv +microns" to plot inverse microns. The various identifiers may be +abbreviated as words but the syntax is not sophisticated enough to +recognized standard scientific abbreviations except as noted below. + +.nf + Table 1: Unit Types + + angstroms - Wavelength in Angstroms + nanometers - Wavelength in nanometers + millimicrons - Wavelength in millimicrons + microns - Wavelength in microns + millimeters - Wavelength in millimeters + centimeter - Wavelength in centimeters + meters - Wavelength in meters + hertz - Frequency in hertz (cycles per second) + kilohertz - Frequency in kilohertz + megahertz - Frequency in megahertz + gigahertz - Frequency in gigahertz + m/s - Velocity in meters per second + km/s - Velocity in kilometers per second + ev - Energy in electron volts + kev - Energy in kilo electron volts + mev - Energy in mega electron volts + z - Redshift + + nm - Wavelength in nanometers + mm - Wavelength in millimeters + cm - Wavelength in centimeters + m - Wavelength in meters + Hz - Frequency in hertz (cycles per second) + KHz - Frequency in kilohertz + MHz - Frequency in megahertz + GHz - Frequency in gigahertz + wn - Wave number (inverse centimeters) +.fi + +The velocity and redshift units require a trailing value and unit defining the +velocity zero point. For example to plot velocity relative to +a wavelength of 1 micron the unit string would be: + +.nf + km/s 1 micron +.fi + +Some additional examples of units strings are: + +.nf + milliang + megahertz + inv mic + log hertz + m/s 3 inv mic + z 5015 ang +.fi +.ih +SEE ALSO +apextract, longslit, rv, imred, specwcs +.endhelp |