Spectrum
spectra
specnum
specband
specdir
linefit
skynum
skyband
Process Spectrum
obj_plot
fixbad
badlines
renormalize
contsub_plot
Find Emission Lines
st_lambda
end_lambda
nsmooth
vel_init
czguess
cortemp
wspan
emsearch
emlines
linedir
vel_init
npfit
linesig
Fit Emission Lines
emcombine
esmooth
mincont
nlcont
velfit
Combine Lines for Redshift
lsmin
lwmin
lwmax
velcorr
sigline
Save Results
report_mode
archive
save_vel
verbose
logfiles
Display Results
vel_plot
dispmode
dispabs
ablines
dispem
displot
device
curmode
hardcopy
plotter
Debugging
debug
cursor
- 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)
-
- 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
-
- 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.
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)
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.
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.
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.
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.
ablines
archive
badlines
contsub_plot
cortemp
czguess
curmode
cursor
debug
device
dispabs
dispem
displot
dispmode
emcombine
emlines
emsearch
esmooth
end_lambda
fixbad
hardcopy
linedir
linefit
linesig
logfiles
lsmin
lwmin
lwmax
mincont
nlcont
npfit
obj_plot
plotter
renormalize
report_mode
save_vel
sigline
skyband
skynum
nsmooth
specband
specdir
specnum
spectra
st_lambda
vel_corr
velfit
vel_init
vel_plot
verbose
wspan
[rvsao]
[emsao]
Last updated 16 July 2020 by Jessica Mink