Spectrum [contents] [index] [procedure]

spectra ""

List of file names of spectra to analyze. @filename indicates list should come from file filename. As of version 1.3, apertures of multispec spectrum files can be entered as numbers, lists, or ranges enclosed in brackets after each file name in the list or file.

specnum 0

If this is nonzero and spectra contains a single file name, this is a range of apertures in a multispec file in which emission lines will be fit. This number is ignored if a spectrum number is specified using brackets. Wavelength dispersion information is read from APNUMn or the WCS keywords. Velocity information is read from APVELn and saved in APVELn and APVEMn.

specband 0

If this is nonzero, it is the band in the multispec file(s) specified by spectra in which emission lines will be fit. Wavelength dispersion information is read from APNUMn, where n is the aperture specified by specnum or the WCS keywords. Velocity information is read from APVELn and saved in APVELn and APVEMn. (New in version 2.0)

specdir "./"

Directory containing spectrum to be analyzed. This part of the pathname is not printed at the top of the page, and is assumed to be the same for all spectra listed in the spectra parameter.

linefit yes

If yes, search for emission lines, fit their positions, and average them into a weighted mean velocity for the spectrum. If no, display spectrum with labelled emission lines found in a previous application of EMSAO and results from any previous XCSAO run which is archived in the image header.

skynum 0

If this is nonzero, the sky spectrum, which is used for equivalent width errors, is read from this spectrum number of the current spectrum file. Wavelength dispersion information is read from APNUMn or the WCS keywords.

skyband 0

If this is nonzero, it is the band in the multispec file(s) specified by spectra from which a sky spectrum will be read to get noise statistics. Wavelength dispersion information is read from APNUMn, where n is the aperture specified by specnum or the WCS keywords. (New in version 2.0)

Process Spectrum [contents] [index]

obj_plot yes

If yes, a plot of the object spectrum is displayed before the emission line search is conducted.

renormalize no

Renormalize spectrum before fitting (yes or no). Set this to "yes" for fluxed spectra.

fixbad no

If "yes", remove wavelength-delimited regions listed in the file specfied by badlines. (added in version 2.0)

badlines badlines.dat

File containing list of starting and stopping wavelengths in Angstroms for removal of portions of all object spectra if fixbad is yes. All information after the second wavelength is a comment field. This file is assumed to be in the directory linedir unless a complete pathname starting with "/" is specified. (added in version 2.0)

contsub_plot no

Plot the continuum-subtracted data if yes

Find Emission Lines [contents] [index] [procedure]

st_lambda INDEF

Starting wavelength in angstroms of portion of spectrum to correlate. If INDEF, use beginning of wavelength overlap between template and spectrum.

end_lambda INDEF

Ending wavelength in angstroms of portion of spectrum to correlate. If INDEF, use end of wavelength overlap between template and spectrum.

nsmooth 10

Number of times the spectrum is smoothed using a 1-2-1 sliding box before the emission line search occurs. This smoothed spectrum is also the version which is displayed.

vel_init "search"

The type of velocity to be used for the initial guess at where the emission lines should be.

If "search", look for the lines in the emsearch file.

If "guess", use czguess as km/sec.

If "zguess", use czguess as z (delta lambda / lambda) (added in 2.0)

If "correlation", use the CZXC parameter in the file header which was set by XCSAO.

If "cortemp", use the velocity from the template entry for the template specified by cortemp which has been set by a XCSAO. (added in 2.0)

If "emission", use the CZEM file header parameter which was set by a previous run of EMSAO.

If "file", use the VELOCITY parameter from the header, a combined velocity which is set by both EMSAO and XCSAO.

czguess 0.

Initial guess at the radial velocity in km/sec (cz) if vel_init is "guess" and in z (delta lambda / lambda) if vel_init is "zguess".

cortemp ""

If vel_init is "cortemp", read the intial guess at the radial velocity in km/sec (cz) from the header entry written by XCSAO for this template. (added in 2.0)

emsearch "emsearch.dat"

File containing list of emission lines used to determine an initial velocity guess if vel_init is "search". This file is assumed to be in the directory linedir unless a complete pathname starting with "/" is specified.

emlines "emlines.dat"

File containing list of emission lines for which to search. The wavelengths in this file are also used to label, in the summary graph, those lines which are found. This file is assumed to be in the directory linedir unless a complete pathname starting with "/" is specified.

linedir "rvsao$lib/"

This directory is the default location for the line list files named by emsearch, emlines, emcombine, ablines, and badlines. Filenames containing a "/" in the first column are assumed to be full pathnames; if there is a "/" anywhere else in the filename, the path is assumed to be relative to the current working directory. If there is a "$" in the filename, the part preceding the "$" is assumed to be an IRAF environment parameter defining a directory. In any of these cases, the linedir parameter is ignored.

linesig 1.5

A line peak must be this many standard deviations above the continuum to qualify as a line. Lower it if obvious lines are not found. Raise it if emsao finds lines made out of noise.

npfit 2

Number of pixels to fit around line peak (+-) for line identification.

wspan 10.

Wavelength in angstroms to search around redshifted line center. This should always be less than the distance between the closest lines for which you are searching.

Fit Emission Lines [contents] [index] [procedure]

emcombine "emcombine.dat"

File containing list of groups of emission lines which should be fit together. Even if the lines are separated, they should be put in the combination file if the program could confuse them. This file is assumed to be in the directory linedir unless a complete pathname starting with "/" is specified.

esmooth 0

Number of times the spectrum is smoothed using a 1-2-1 sliding box before the emission lines are fit. Normally 0, it can be set to 1 or 2 for very noisy data when the fitting subroutine may otherwise be unable to fit a continuum. It should be set no higher to avoid distorting the emission line profiles.

mincont 0.0

If continuum is greater than this value, compute the equivalent width of the current line, which is the width the line would be if it were as high as the continuum is deep. If the continuum is less than or equal to this value, compute the area of the line in counts times wavelength. When working with continuum subtracted spectra or spectra where the emission lines are so strong that there is minimal continuum, make this value larger than the largest possible continuum fit value to get consistently computed numbers. (added in 2.0)

nlcont 1

Number of coefficients in line continuum fit (0-3). An overall continuum fit is subtracted, but the fit may not be good enough to remove the local continuum. If 0, no additional continuum is fit for each line.

velfit yes

If yes, combine the redshifts found for individual emission lines into a single emission line velocity. (eliminated from 1.8 on)

Velocity Modification [contents] [index] [procedure]

lwmin 0.4

Minimum fraction of mean line width for individual line. (added in 2.0)

lwmax 1.7

Maximum fraction of mean line width for individual line. (added in 2.0)

lsmin 1.0

Minimum equivalent width in sigma for individual line. (added in 2.0)

vel_corr "file"

Spectrum velocity correction to the solar system barycenter. Set to "none" if spectrum has already been shifted or if this correction is unnecessary. If "file", BCV is used if present in the file header, or else HCV. If "hfile", the header parameter HCV is always used. If neither is found, no correction is made. If "heliocentric" or "barycentric" corrections are chosen, position and time parameters are read from the spectrum data file header. DATE-OBS (date in format 'dd-mm-yy') UT (U.T. at end of exposure as 'hh:mm:ss') and UTOPEN (U.T. at start of exposure as 'hh:mm:ss') or EXPOSURE (length of exposure in seconds) are used to compute the midtime of the exposure. RA (right ascension as 'hh:mm:ss.ss'), DEC (declination as 'dd:mm:ss.ss'), and EPOCH (epoch of coordinates defaults to 1950.0) give the position of the object whose spectrum this is. SITELONG (observatory longitude as 'dd:mm:ss.ss' or degrees), SITELAT (observatory latitude as 'dd:mm:ss.ss' or degrees), and SITEELEV (observatory altitude in meters) give the observatory position.

sigline 0.0

Velocity error if single line found. Use gaussian fit error if 0 or INDEF. This value may need to be set higher to use a good, but different cross-correlation properly when the program computes a combined velocity.

Save Results [contents] [index] [procedure]

report_mode 1

Mode in which results of emission line fits are reported. By default, columns are separated by single spaces, but if report_mode is negated, tabs are used instead.

=1 Full information on each emission line found

=2 One line per spectrum, with combined, cross-correlation, and emission line velocities, number of lines found and fit, and a list of names and wavelengths of the lines which were used in the fit.

=3 One line per spectrum, with combined, cross-correlation, and emission line velocities, number of lines found and fit, and velocities for all possible reference lines, with velocities of lines not used in the final velocity fit set to 0.

=4 One line per spectrum, with file name, instrument, object, right ascension, declination, altitude, azimuth, Julian date, exposure, emission velocity and error, cross-correlation velocity, error, and R-value (for the template specified by cortemp or best template value if cortemp is ""), and the combined velocity and error. Following the number of lines found and the number of lines fit, the velocity, error, height, width, and equivalent width are then given for each line, with zero values indicating that the line was not used in the fit. If the continuum under the line is less than mincont, the area of the line is given instead of the equivalent width.

=5 One line per spectrum, with combined, cross-correlation (for the template specified by cortemp, and emission line velocities, number of lines found and fit, and a list of names and wavelengths of the lines which were used in the fit.

=6 One line per spectrum, with combined, cross-correlation (for the template specified by cortemp, and emission line velocities, number of lines found and fit, and velocities for all possible reference lines. Velocities of lines not used in the final velocity fit are set to zero.

=7 One line per spectrum, with file name, instrument, object, right ascension, declination, altitude, azimuth, Julian date, exposure, emission velocity and error, cross-correlation velocity, error, and R-value (for the template specified by cortemp or best template value if cortemp is ""), and the combined velocity and error. Following the number of lines found and the number of lines fit, the velocity, error, height, width, equivalent width, and equivalent width error are then given for each line, with zero values indicating that the line was not used in the fit. If the continuum under the line is less than mincont, the area of the line is given instead of the equivalent width. This mode is the same as mode 4, with the addition of the error in equivalent width for each line.
(added in version 2.2)

=8 One line per spectrum, with file name, instrument, object, right ascension, declination, altitude, azimuth, Julian date, and exposure. Following the number of lines found and the number of lines fit, the wavelength shift and error in Angstroms, height, width in Angstroms, equivalent width, and equivalent width error are then given for each line, with zero values indicating that the line was not used in the fit. If the continuum under the line is less than mincont, the area of the line is given instead of the equivalent width.
(added in version 2.2.0)

=9 Full information on each emission line found, adding equivalent width errors One line per spectrum, with combined, cross-correlation, and emission line velocities, number of lines found and fit, and a list of names and wavelengths of the lines which were used in the fit. (added in version 2.2.0)

=10 Mode 1 information on each emission line found, adding equivalent width errors (added in version 2.2.4)

=11 Single line report with one velocity per possible line # For comparison spectra, print file path, date, and # line shifts in vel(14), pix(15), or angstroms(16) (added in version 2.4.3)

=12 For echelle spectra, print more emission lines with more precision. (added in version 2.6.4)

=13 Print full pathname and line information on one long line (added in version 2.8.4)

=14 Print full pathname, Julian date, number of lines searched for, number found, line shifts in velocity on one line (added in version 2.8.4)

=15 Print full pathname, Julian date, number of lines searched for, number found, line shifts in wavelength on one line (added in version 2.8.4)

=16 Print full pathname, Julian date, number of line searched for, number found, line shifts in pixels on one line (added in version 2.8.4)

archive no

If yes, save emission line results in SAO TDC archive record.

save_vel no

If yes, save results in the IRAF image header, in a compact form if specnum is greater than zero; otherwise in a more expanded form.

verbose yes

If yes, results of the emission line search are logged to logfiles.

logfiles "STDOUT,emsao.log"

All results from EMSAO are recorded in these files.

Display Information [contents] [index] [procedure]

dispmode 2

Graphical display mode ( 2=with line list or 3=full screen)

displot yes

If yes, graph data on device.

vel_plot "emission"

The redshift of this velocity is used to compute the positions of the absorption and emission lines which are flagged in the display. Choices are emission, correlation, or combination (a weighted combined velocity saved as the VELOCITY keyword in the spectrum header). The chosed velocity is flagged with a * on the upper right portion of the summary graph.

ablines "ablines.dat"

File containing list of absorption lines for which the positions should be indicated on the summary graph. This file is assumed to be in the directory linedir unless a complete pathname starting with "/" is specified.

dispem yes

If yes, flag positions of emission lines which have been found. Those used in the velocity fit are plotted as solid lines. The "-" cursor command can be used to delete these from the fit. Those lines found but omitted from the fit are plotted as dashed lines. The "+" cursor command can be used to add them to the fit.

dispabs yes

If yes, flag positions of all absorption lines within wavelength range plotted.

device "stdgraph"

Device on which to display graphic summary of results.

hardcopy no

Print graphic summary of results on plotter.

plotter "stdplot"

Bf hardcopy is yes, make hardcopies of graphs on this device.

curmode yes

If yes, stop in cursor mode after plotting and labelling spectrum and wait for cursor commands.

Debugging [contents] [index]

debug no

If yes, intermediate values of the parameters are recorded in the log files. Too much information is printed to be useful for anything but debugging.

cursor ""

Graphics cursor input. When null the standard cursor is used otherwise the specified file is used.

EMSAO Parameters, Alphabetically

[rvsao] [emsao]

Last updated 16 July 2020 by Jessica Mink