package: Discussion and overview of package including sections on:

Package: onedspec

Usage

onedspec

Parameters

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 observatory.observatory, or "obspars" to select the current parameters set in the observatory task. See help for observatory for additional information.

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.

interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc)

Spectrum interpolation type used when spectra are resampled. The choices are:

nearest - nearest neighbor
 linear - linear
  poly3 - 3rd order polynomial
  poly5 - 5th order polynomial
spline3 - cubic spline
   sinc - sinc function

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.

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.

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.

records = ""

This is a dummy parameter. It is applicable only in the imred.irs and imred.iids packages.

version = "ONEDSPEC V3: November 1991"

Package version identification.

Description

The onedspec 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 onedspec package with applicable tasks are summarized in Table 1.

Table 1: Functions provided in the onedspec package

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

There are other packages which provide additional functions or specialized tasks for spectra. Radial velocity measurements are available in the noao.rv package. The noao.imred package contains a number of packages for specific types of data or instruments. These packages are listed in Table 2.

Table 2: Imred spectroscopy packages

    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

Finally, there are non-NOAO packages which may contain generally useful software for spectra. Currently available packages are stsdas and xray.

Spectrum image formats and coordinate systems

See the separate help topic specwcs.

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 dispcor, sarith, scombine, and splot.

The interpolation type is set by the package parameter interp. The available interpolation types are:

nearest - nearest neighbor
 linear - linear
  poly3 - 3rd order polynomial
  poly5 - 5th order polynomial
spline3 - cubic spline
   sinc - sinc function

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.

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, splot and specplot, 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.

        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)

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:

km/s 1 micron

Some additional examples of units strings are:

milliang
megahertz
inv mic
log hertz
m/s 3 inv mic
z 5015 ang

See also

apextract, longslit, rv, imred, specwcs