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apfit noao.twodspec.apextract



apfit -- Fit 2D spectra using APEXTRACT profile algorithms


apfit input output fittype


List of input images to be fit.
output = ""
List of output images to be created with the fitting results. If the null string is given or the end of the output list is reached before the end of the input list then the input image name is used and an extension of ".fit", ".diff", or ".ratio" is added based on the type of fit.
apertures = ""
Apertures to recenter, resize, trace, and fit. This only applies to apertures read from the input or reference database. Any new apertures defined with the automatic finding algorithm or interactively are always selected. The syntax is a list comma separated ranges where a range can be a single aperture number, a hyphen separated range of aperture numbers, or a range with a step specified by "x<step>"; for example, "1,3-5,9-12x2".
fittype = "difference"
Type of fitted output. The choices are:
The fitted spectra are output.
The difference (or residuals) of the data and the fit (data - fit).
The ratio of the data to the fit. If a fitted pixel goes below a specified threshold the ratio is set to 1.
references = ""
List of reference images to be used to define apertures for the input images. When a reference image is given it supersedes apertures previously defined for the input image. The list may be null, "", or any number of images less than or equal to the list of input images. There are three special words which may be used in place of an image name. The word "last" refers to the last set of apertures written to the database. The word "OLD" requires that an entry exist and the word "NEW" requires that the entry not exist for each input image.

interactive = yes
Run this task interactively? If the task is not run interactively then all user queries are suppressed and interactive aperture editing and trace fitting are disabled.
find = yes
Find the spectra and define apertures automatically? In order for spectra to be found automatically there must be no apertures for the input image or reference image defined in the database.
recenter = yes
Recenter the apertures?
resize = yes
Resize the apertures?
edit = yes
Edit the apertures? The interactive parameter must also be yes.
trace = yes
Trace the apertures?
fittrace = yes
Interactively fit the traced positions by a function? The interactive parameter must also be yes.
fit = yes
Fit the spectra and produce a fitted output image?

The following two parameters are used in the finding, recentering, resizing, editing, and tracing operations.

line = INDEF
The starting dispersion line (line or column perpendicular to the dispersion axis) for the tracing. A value of INDEF starts at the middle of the image.
nsum = 1
Number of dispersion lines to be summed or medianed at each step along the dispersion. For tracing only summing is done and the sign is ignored.

threshold = 10.
Division threshold for ratio fit type. If a pixel in the fitted spectrum is less than this value then a ratio of 1 is output.

The following parameters control the profile and spectrum fitting.

background = "none"
Type of background subtraction. The choices are "none" for no background subtraction, "average" to average the background within the background regions, or "fit" to fit across the dispersion using the background within the background regions. Note that the "average" option does not do any medianing or bad pixel checking; it is faster than fitting however. Background subtraction also requires that the background fitting parameters are properly defined. For the "average" option only the background sample regions parameter is used.
pfit = "fit1d" (fit1d|fit2d)
Profile fitting algorithm to use with variance weighting or cleaning. When determining a profile the two dimensional spectrum is divided by an estimate of the one dimensional spectrum to form a normalized two dimensional spectrum profile. This profile is then smoothed by fitting one dimensional functions, "fit1d", along the lines or columns most closely corresponding to the dispersion axis or a special two dimensional function, "fit2d", described by Marsh (see approfile ).
clean = no
Detect and replace deviant pixels?
skybox = 1
Box car smoothing length for sky background when using background subtraction. Since the background noise is often the limiting factor for good extraction one may box car smooth the sky to improve the statistics in smooth background regions at the expense of distorting the subtraction near spectral features. This is most appropriate when the sky regions are limited due to a small slit length.
saturation = INDEF
Saturation or nonlinearity level. During variance weighted extractions wavelength points having any pixels above this value are excluded from the profile determination.
readnoise = 0.
Read out noise in photons. This parameter defines the minimum noise sigma. It is defined in terms of photons (or electrons) and scales to the data values through the gain parameter. A image header keyword (case insensitive) may be specified to get the value from the image.
gain = 1
Detector gain or conversion factor between photons/electrons and data values. It is specified as the number of photons per data value. A image header keyword (case insensitive) may be specified to get the value from the image.
lsigma = 3., usigma = 3.
Lower and upper rejection thresholds, given as a number of times the estimated sigma of a pixel, for cleaning.


I/O parameters and the default dispersion axis are taken from the package parameters, the default aperture parameters from apdefault , automatic aperture finding parameters from apfind , recentering parameters from aprecenter , resizing parameters from apresize , parameters used for centering and editing the apertures from apedit , and tracing parameters from aptrace .


The two dimensional spectra within the defined apertures of the input images are fit by a model and new output images are created with either the model spectra, the difference between the input and model spectra, or the ratio of input and model spectra. The type of output is selected by the parameter fittype which may have one of the values "fit", "difference", or "ratio".

Aperture definitions may be inherited from those of other images by specifying a reference image with the references parameter. Images in the reference list are matched with those in the input list in order. If the reference image list is shorter than the number of input images, the last reference image is used for all remaining input images. Thus, a single reference image may be given for all the input images or different reference images may be given for each input image. The special reference name "last" may be used to select the last set apertures used in any of the apextract tasks.

If an aperture reference image is not specified or no apertures are found for the specified reference image, previously defined apertures for the input image are sought in the aperture database. Note that reference apertures supersede apertures for the input image. If no apertures are defined they may be created automatically, the find option, or interactively in the aperture editor, if the interactive and edit options are set.

The functions performed by the task are selected by a set of flag parameters. The functions are an automatic spectrum finding and aperture defining algorithm (see apfind ) which is ignored if apertures are already defined, automatic recentering and resizing algorithms (see aprecenter and apresize ), an interactive aperture editing function (see apedit ), a spectrum position tracing and trace function fit (see aptrace ), and the main function of this task, two dimensional model fitting.

Each function selection will produce a query for each input spectrum if the interactive parameter is set. The queries are answered by "yes", "no", "YES", or "NO", where the upper case responses suppress the query for following images. There are other queries associated with tracing which first ask whether the operation is to be done interactively and, if yes, lead to queries for each aperture. If the interactive parameter is not set then aperture editing and interactive trace fitting are ignored.

The two dimensional spectrum model consists of a smooth two dimensional normalized profile multiplied by the variance weighted one dimensional spectrum. The profile is computed by dividing the data within the aperture by the one dimensional spectrum, smoothing with either low order function fits parallel to the dispersion axis or a special two dimensional function as selected by the pfit parameter. The smooth profile is then used to improve the spectrum estimate using variance weighting and to eliminate deviant or cosmic ray pixels by sigma tests. The profile algorithm is described in detail in approfiles and the variance weighted spectrum is described in apvariance .

The process of determining the profile and variance weighted spectrum, and hence the two dimensional spectrum model, is identical to that used for variance weighted extraction of the one dimensional spectra in the tasks apall or apsum . Most of the parameters of in this task are the same as those in the extraction tasks and so further information about them may be found in the descriptions of those tasks.

Because of the connection with variance weighted extraction and cleaning of one dimensional spectra, this task is useful as a diagnostic tool for understanding and evaluating the variance weighting algorithm. For example the "difference" image provides the residuals in a two dimensional visual form.

The "fit" output image does not include any background determination; i.e the fit is background subtracted. Pixels outside the modeled spectra are set to zero.

The "difference" output image is simply the difference between the background subtracted "fit" and the data. Thus the difference within the apertures should approximate the background and outside the apertures the difference will be identical with the input image.

The "ratio" output image does include any background in the model before taking the ratio of the data and model. If a model pixel is less than the given threshold parameter the output ratio is set to one. This is used to avoid division by zero and set a limit to noise in ratio image. Outside of the apertures the ratio output pixels are set to one.


1. To compute the residuals of a model fit where the image already has aperture defined:

cl> apfit ls1 inter- rec- res- trace- read=3 gain=1 back=fit


The "apertures" parameter can be used to select apertures for resizing, recentering, tracing, and extraction. This parameter name was previously used for selecting apertures in the recentering algorithm. The new parameter name for this is now "aprecenter".


apbackground, approfile, apvariance, apdefault, apfind, aprecenter, apresize, apedit, aptrace, apsum, apall

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