Basic Information on mbspect

Task: mbspect
Purpose: Make spectrum and measure velocities from a Miriad image.
Categories: image analysis and display.

MBSPECT makes an spectrum of the velocity or frequency axis of a
Miriad image. The spectrum is integrated, averaged or beam-weighted,
over the width specified, for the other image axes. Robust spectral
baselines can be fitted, and the profile parameterised (velocities,
widths, moments). The output spectrum can be plotted and/or written
out as a miriad and/or ascii file for further analysis.

Key: in
The input image. vxy and xyv images are acceptable inputs. 
No default.

Key: out
The output spectrum, if required. Spectral units are always in the
same units as the input file (even if a conversion is performed for
the plot and/or log file). This spectrum can be read back into
MbSpect. 

Key: coord
The position, in world coordinates, for which the spectrum is
required, e.g. coord=12:00:13,-42:00:43. The cube must have
an RA and a DEC axis. The pixel with the nearest position is
chosen. The default is the centre of the image (not necessarily
the reference pixel).

Key: width
Two numbers, being the spatial width of the box in pixels (in RA
and DEC) within which the spectrum is averaged (or integrated).
Must be odd numbers. Default is 1,1.

Key: xaxis
The x-axis can be plotted as 'channel', 'frequency' ('FREQ'), 
'optical' velocity ('FELO'),  'radio' velocity ('VELO'), or the units
in the image. The default which is whatever units are in the header.

Key: yaxis
If 'average' then the pixels enclosed in the x-y area specified
are averaged. If 'sum' they are summed and normalized if the units
are known. If 'point' they are optimally weighted according to 
the beam parameters, assuming that the source is unresolved.
Default is 'average'

Key: xrange
X-axis range for plot. The default is to self-scale to the region
requested. The units are km/s for velocity and MHz for frequency
(i.e. not the normal miriad convention).

Key: yrange
Y-axis range for plot. The default is to self-scale.

Key: hann
Hanning smoothing length (an odd integer < 15). The default is
no smoothing (hann = 1).

Key: order
Order of optional robust (clipped polynomial) fit (0-10) to be applied
to the spectral axis. If the order is positive (0 to 10), the fit is
plotted on top of the data; if negative (-0 to -10), the fit is
subtracted before plotting. The fit is always subtracted from any 
output data written. (For bulk removal of baselines in a cube, use 
contsub). Default is no fit.

Key: options
List of minimum match task enrichment options.
1deriv  Take 1-sided derivative of spectrum before plotting
        and after Hanning smoothing. Useful for Zeeman enthusiasts.
2deriv  Take 2-sided derivative of spectrum before plotting.
histo   Plot the spectrum as a histogram instead of joining points.
pstyle1 Alternative plot style, where the object and position
        information is omitted and the comment field is centered
        at the top of the plot. Typically, this is used for
        publication-quality plots (the source name, if required.
        should be inserted into the comment field).
pstyle2 Alternative plot style, where the object and position
        information is omitted, the comment field is centered
        at the top of the plot (as with options=pstyle1), and
        the x and y axis labels are omitted. Typically, this is 
        used to generate publication-quality n x m matrix plots
        (the source name, if required should be inserted into 
        the comment field).
posfit  If width>1, a source position is estimated from a Gaussian
        fit to the moment map. The moment map is formed using the 
        velocity range specified by the profile parameter. If
        yaxis=point, this new position is used when forming
        the spectrum (the region set by the initial coord 
        parameter and the width parameter is not changed).
measure Measure various spectral parameters on plotted spectrum.
        If a profile window is set, the line is only measured 
        within this window. If the order keyword is used, the fit
        is always subtracted before spectral fitting. If a plot
        device is selected, the width-maximised 50% and 20% points
        are highlighted with a circle and the width-minimised
        points are highlighted with a cross. Zeroth moment (profile
        area), first moment (mean velocity/frequency/channel) and
        second moment (dispersion) are calculated in the usual way.
        These parameters are not robust unless careful use of the
        profile and clip parameters is made. However, more
        robust moment-like parameters are also calculated by using an
        algorithm which minimises the mean absolute deviation of
        the flux-weighted velocities

Key: clip
Two values. Exclude pixels with values in the range clip(1) to clip(2).
If only one value is given, then exclude -abs(clip) to abs(clip).

Key: mask
This specifies the x-axis ranges to be excluded from any
continuum fit, e.g. those containing line emission. It consists 
of a number of pairs, each pair giving a start and end x-value. 
The default is that all channels are line-free, which is quite a 
good approximation if the line is weak compared to the continuum. 
The units of the x-axis values are the same as given by the xaxis
keyword.

Key: profile
Two values. This specifies the x-axis range to be included for
profile measurement (options=measure). It consists of a start
and end x-value. The default is that all channels are used for
profile measurement. For weak lines, you will normally need to 
set a profile window, a mask window a clip level, or any 
combination of the above. The profile and mask windows may be 
the same, although the profile window is limited to a single pair 
of values. The units of the x-axis values are the same as given 
by the xaxis keyword.

Key: device
Standard PGPLOT device. See the help on device for more information.

Key: csize
Up to 2 values. Character sizes in units of the PGPLOT default
(which is ~ 1/40 of the view surface height) for the plot axis
labels and the title.
Defaults try to choose something sensible.  Use 0.0 to default
any particular value.

Key: log
Write spectrum to this ascii file. Spectral axis units are as
specified by the xaxis keyword. Default is no output file.

Key: comment
A one-line comment which is written into the logfile and any plot.

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