From fa080de7afc95aa1c19a6e6fc0e0708ced2eadc4 Mon Sep 17 00:00:00 2001
From: Joseph Hunkeler <jhunkeler@gmail.com>
Date: Wed, 8 Jul 2015 20:46:52 -0400
Subject: Initial commit

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 noao/twodspec/apextract/doc/apbackground.hlp | 79 ++++++++++++++++++++++++++++
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+.help apbackground Aug90 noao.twodspec.apextract
+
+.ce
+Background Determination
+
+
+Data from slit spectra allow the determination and subtraction
+of the background sky using information from regions near the object
+of interest.  Background subtraction may also apply to cases of
+scattered light though other techniques for scattered light removal
+may be more appropriate.  The APEXTRACT package provides for determining
+the background level at each wavelength (line or column along the dispersion
+axis) from a set of regions and extrapolating and subtracting the
+background at each pixel extracted from the object profile.  The
+type of background used during extraction is specified by the parameter
+\fIbackground\fR.  If the value "none" is used then no background is
+subtracted and any background parameters defined for an aperture are
+ignored.  If the value is "average", "median", "minimum" or "fit" then a
+background is determined, including a variance estimate when using variance
+weighted extraction (see \fIapvariance\fR), and the subtracted background
+spectrum may be output if the \fIextras\fR parameter is set.
+
+The basic aperture definition structure used in the APEXTRACT package
+includes associated background regions and fitting parameters.  The
+background regions are specified by a list of colon delimited ranges
+defined relative to the center of the aperture.  There are generally
+two ranges, one on each side of the object, though one sided or more
+complex sets may be used to avoid contaminated or missing parts
+of the slit.  The default ranges are defined by the parameter
+\fIb_sample\fR.  Often the ranges are better set graphically using a
+cursor by invoking the 'b' option of the aperture editor.
+
+If the background type is "average", "median", or "minimum" then pixels
+occupying these regions are averaged, medianed, or the minimum found to
+produce a single background level for all object pixels at each wavelength.  
+Note that the "average" choice does not exclude any pixels which may
+yield a background contaminated by cosmic rays.  The "median" or "minimum"
+is recommended instead.
+
+If the background type is "fit" then a function is fit to the pixels in the
+background regions using the ICFIT options (see \fBicfit\fR).  The
+parameter \fIb_naverage\fR may be used to compute averages or medians of
+groups or all of the points within each sample region.  The fit is defined
+by a function type \fIb_function\fR; one of legendre polynomial, chebyshev
+polynomial, linear spline, or cubic spline, and function order
+\fIb_order\fR (number of polynomial terms or spline pieces).  An
+interactive rejection of grossly deviant points from the fit may also be
+used.  The fitted function can define a constant, sloped, or higher order
+background for the object pixels.
+
+Note that the background setting function, the 'b' key in \fBapedit\fR,
+may be used to set the background regions for all the background options
+but it will always show the result of a fit regardless of the background
+type.
+
+After determining a background by averaging, medianing, minimizing, or
+fitting, a box car smoothing step may be applied.  The box car size is
+given by the parameter \fIskybox\fR.  When the number of available
+background pixels is small, due to a small slit for instance, the noise
+introduced to the extracted object spectrum may be unsatisfactorily large.
+By smoothing the background one can reduce the noise when the background
+consists of a smooth continuum.  The trade-off, however, is that near sharp
+features the smoothing will smear the features out and give a poorer
+subtraction of these features.  One could extract both the object and
+background separately and apply a background smoothing separately using
+other image processing tools.  However, this is not possible for variance
+weighted extraction because of the intimate connection between the
+background levels, the profile determination, and the variance estimates
+based on both.  Thus, this smoothing feature is included.
+
+The background determined by the methods outlined above is actually
+subtracted as a separate step during extraction.  The background
+is also used during profile fitting when cleaning or using variance
+weighted extraction.  See \fBapvariance\fR and \fBapprofile\fR for
+further discussion.
+.ih
+SEE ALSO
+approfile apvariance apdefault icfit apall apsum
+.endhelp
-- 
cgit 

