.help msextract Jul84 noao.twodspec.multispec
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NAME
msextract -- Extract spectra from a multi-spectra image
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USAGE
msextract image output
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PARAMETERS
.ls image
Image to be extracted.
.le
.ls output
Filename for the three dimensional image to be created containing the
extracted spectra.
.le
.ls lower = -10
Lower limit of the integral for integrated spectra or the first column of the
strip spectra.  It is measured in pixels from the spectrum center
defined by the position function in the MULTISPEC database.
.le
.ls upper = 10
Upper limit of the integral for integrated spectra or (approximately) the
last column of the strip spectra.  It is measured in pixels from the
spectrum center defined by the position function in the MULTISPEC database.
.le
.ls spectra = "*"
Spectra to be extracted.
.le
.ls lines = "*"
Image lines to be extracted.
.le
.ls ex_model = no
Extract model spectra fit to the image spectra?
.le
.ls integrated = yes
Extract integrated spectra?
.le
.ls unblend = no
Correct for blending in the extracted spectra?
.le
.ls clean = yes
Replace bad pixels with model values?  The following parameters are used:
.ls  nreplace = 1000.
Maximum number of pixels to be replaced per image line when cleaning with
model \fIgauss5\fR or maximum number of pixels to be replaced per spectrum when
cleaning with model \fIsmooth\fR.
.le
.ls sigma_cut = 4.
Cleaning threshold in terms of sigma of the fit.
.le
.ls niterate = 1
Maximum number of cleaning iterations per line when cleaning with model
\fIgauss5\fR.
.le
.le
.ls model = "smooth"
Choice of \fIgauss5\fR or \fIsmooth\fR.  Minimum match abbreviation is
allowed.  This parameter is required only if \fIex_model\fR = yes
or \fIclean\fR = yes.
.le
.ls naverage = 20
Number of lines to be averaged in model \fIsmooth\fR.
.le
.ls fit_type = 2
Model fitting algorithm for model \fIgauss5\fR.
.le
.ls interpolator = "spline3"
Type of image interpolation function to be used.
The choices are "nearest", "linear", "poly3", "poly5", and "spline3".
Minimum match abbreviation is allowed.
.le
.ls verbose = no
Print verbose output?
.le
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DESCRIPTION
The MULTISPEC database describing the spectra positions and shapes
is used to guide the extraction of the spectra in the multi-spectra image.
The user selects the \fIspectra\fR and image
\fIlines\fR to be extracted and whether to extract integrated or strip spectra.
In addition options are available to extract model spectra, replace bad
pixels by model spectra values, and correct for blending of the spectra.
The \fIoutput_file\fR three dimensional
image consists of one band (the third dimension) per extracted spectrum,
the extracted lines (the second dimension) and either one column for
the integrated luminosity or the number of columns in the extracted strip.

Integrated spectra (\fIintegrated\fR = yes) are extracted by summing
the pixel or model values over the specified limits \fIlower\fR and \fIupper\fR
measured relative to the spectra centers defined by the position functions in
the database.  Partial pixel sums are used at the endpoints.

Strip spectra (\fIintegrated\fR = no) are extracted by image interpolation
of the image line or model profiles to obtain a line of values for
each spectrum and for each image line.  The length of the strip is the
smallest integer containing the interval between \fIlower\fR and \fIupper\fR.
The strips for each spectrum are aligned so that the first column is a distance
\fIlower\fR from the spectrum center as given by the position function in the
database.

If \fIex_model\fR = yes, \fIunblend\fR = yes, or \fIclean\fR = yes model
spectra are fit to the spectra in the image.  There are two models:
a five parameter Gaussian profile called \fIgauss5\fR and profiles obtained
by averaging \fInaverage\fR image lines surrounding the image line being
modeled called \fIsmooth\fR.  The model is selected either when the parameter
\fIunblend\fR = yes or with the parameter \fImodel\fR.  If \fIunblend\fR = yes
then the model is \fIgauss5\fR regardless of the value of \fImodel\fR.

When \fIex_model\fR = yes the effect is to substitute model spectra for the
image spectra in the output extraction image.

When \fIclean\fR = yes pixels with large residuals from the model are
detected and removed from the model fit.  The selected model is
fit to the pixels which are not in the bad pixel list (not yet implemented)
and which have not been removed from the model fit.  The sigma of the fit
is computed.  Deviant pixels are detected by comparing them to the model
to determine if they differ by more than \fIsigma_cut\fR times the sigma.
The model fit is iterated, removing deviant pixels at each iteration, until
no more pixels are found deviant or \fInreplace\fR pixels have been found.
The pixels removed or in the bad pixel list are then replaced with
model values.  (To clean an image with this algorithm see \fBnewimage\fR.)

There are some technical differences in the model fitting and cleaning
algorithms for the two models.  In model \fIsmooth\fR
the fit for the profile scale factors is done independently for each spectrum
and automatically corrected when a bad pixel is detected.  This fitting process
is fast and rigorous.  The parameter \fInreplace\fR in this model refers to
the maximum number of pixels replaced \fIper spectrum\fR.

In model \fIgauss5\fR, however, the profile scale factors are fit
to the entire image line (hence its ability to fit blended spectra).
There are two fitting algorithms; a rigorous simultaneous fit
and an approximate method.  The simultaneous fit is selected when
\fIfit_type\fR = 1.  This step is relatively slow. The
alternative method of \fIfit_type\fR = 2 sets the scale factor for each
spectrum by taking the median scale, where scale = data / model profile,
for the three pixels nearest the center of the profile.  The median
minimizes the chance of a large error due to a single bad pixel.  This
scale may be greatly in error in the case of extreme blending but is also
quite fast; the extraction time is reduced by at least 40%.
The steps of profile fitting and deviant pixel detection are alternated
and the maximum number of iterations through these two steps is
set by \fIniterate\fR.  The default of 1 means that the model fitting is not
repeated after detecting deviant pixels.

When \fIunblend\fR = yes the \fIgauss5\fR model
is fitted to the image spectra (including possible cleaning).
The relative contributions to the total image pixel value from each of the
blended spectra are determined from the model and applied toward either the
integrated or strip spectra.  If \fIex_model\fR = yes then this option has
no effect other than to force the selection of model \fIgauss5\fR.

The option \fIverbose\fR is used to print the image lines being extracted
and the number of pixels replaced by the cleaning process.
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EXAMPLES
To extract all the integrated spectra from all the image lines:

	cl> msextract image image.ms

To extract model strip spectra:

	cl> msextract image image.ms ex_model=yes int=no

To extract integrated spectra without any modeling:

	cl> msextract image image.ms clean=no
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SEE ALSO
newimage
.endhelp
