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do3fiber noao.imred.kpnocoude



do3fiber -- Three fiber data reduction task


do3fiber objects


The do3fiber reduction task is specialized for scattered light subtraction, extraction, flat fielding, and wavelength calibration of multifiber data in which some fibers are used to take object spectra and other fibers are used to take simultaneous arc spectra. A three fiber instrument of this type (one object and two arc fibers) is available at the KPNO coude feed. The default parameters are set for this configuration. If there are a large number of fibers and fiber throughput and sky fiber subtraction is needed the dofiber task should be used.

The do3fiber task is a command language script which collects and combines the functions and parameters of many general purpose tasks to provide a single complete data reduction path. The task provides a degree of guidance, automation, and record keeping necessary when dealing with this type of multifiber data.


List of object spectra to be processed. Previously processed spectra are ignored unless the redo flag is set or the update flag is set and dependent calibration data has changed. Extracted spectra are ignored.
apref = ""
Aperture reference spectrum. This spectrum is used to define the basic extraction apertures and is typically a flat field spectrum.
flat = "" (optional)
Flat field spectrum. If specified the one dimensional flat field spectra are extracted and used to make flat field corrections.
arcs = "" (at least one if dispersion correcting)
List of primary, all fiber arc spectra. These spectra are used to define the dispersion functions for each fiber apart from a possible zero point correction made with simultaneous arc calibration fibers in the object spectra. One fiber from the first spectrum is used to mark lines and set the dispersion function interactively and dispersion functions for all other fibers and arc spectra are derived from it.
arctable = "" (optional) (refspectra)
Table defining arc spectra to be assigned to object spectra (see refspectra ). If not specified an assignment based on a header parameter, params.sort , such as the observation time is made.

readnoise = "RDNOISE" (apsum)
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 = "GAIN" (apsum)
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.
datamax = INDEF (apsum.saturation)
The maximum data value which is not a cosmic ray. When cleaning cosmic rays and/or using variance weighted extraction very strong cosmic rays (pixel values much larger than the data) can cause these operations to behave poorly. If a value other than INDEF is specified then all data pixels in excess of this value will be excluded and the algorithms will yield improved results. This applies only to the object spectra and not the flat field or arc spectra. For more on this see the discussion of the saturation parameter in the apextract package.
fibers = (apfind)
Number of fibers. This number is used during the automatic definition of the apertures from the aperture reference spectrum.
width = 6. (apedit)
Approximate base full width of the fiber profiles. This parameter is used for the profile centering algorithm.
crval = INDEF, cdelt = INDEF (autoidentify)
These parameters specify an approximate central wavelength and dispersion. They may be specified as numerical values, INDEF, or image header keyword names whose values are to be used. If one or both of these parameters are specified as INDEF the search for a solution will be slower and more likely to fail.
objaps = "2", arcaps = "1,3"
List of object and arc aperture numbers. These are used to identify arc apertures for wavelength calibration and object apertures for the final results.

scattered = no (apscatter)
Smooth and subtracted scattered light from the object and flat field images. This operation consists of fitting independent smooth functions across the dispersion using data outside the fiber apertures and then smoothing the individual fits along the dispersion. The initial flat field, or if none is given the aperture reference image, are done interactively to allow setting the fitting parameters. All subsequent subtractions use the same fitting parameters.
fitflat = yes (flat1d)
Fit the composite flat field spectrum by a smooth function and divide each flat field spectrum by this function? This operation removes the average spectral signature of the flat field lamp from the sensitivity correction to avoid modifying the object fluxes.
recenter = yes (aprecenter)
Recenter reference apertures for each object spectrum?
edit = no (apedit)
Review aperture definitions for each object spectrum? Note that this does not apply to the initial reference aperture which always allows interactive review of the aperture definitions.
clean = no (apsum)
Detect and correct for bad pixels during extraction? This is the same as the clean option in the apextract package. If yes this also implies variance weighted extraction and requires reasonably good values for the readout noise and gain. In addition the datamax parameters can be useful.
dispcor = yes
Dispersion correct spectra? Depending on the params.linearize parameter this may either resample the spectra or insert a dispersion function in the image header.
splot = yes
Plot the final spectra with the task splot ?
redo = no
Redo operations previously done? If no then previously processed spectra in the objects list will not be processed (unless they need to be updated).
update = yes
Update processing of previously processed spectra if aperture, flat field, or dispersion reference definitions are changed?
batch = no
Process spectra as a background or batch job provided there are no interactive options (edit and splot ) selected.
listonly = no
List processing steps but don't process?

params = "" (pset)
Name of parameter set containing additional processing parameters. The default is parameter set params . The parameter set may be examined and modified in the usual ways (typically with "epar params" or ":e params" from the parameter editor). Note that using a different parameter file is not allowed. The parameters are described below.


Package parameters are those which generally apply to all task in the package. This is also true of do3fiber .

observatory = "observatory"
Observatory at which the spectra were obtained if not specified in the image header by the keyword OBSERVAT. For NOAO data the image headers identify the observatory as "kpno" or "ctio" so this parameter is not used. For data from other observatories this parameter may be used as describe in observatory .
interp = "poly5" (nearest|linear|poly3|poly5|spline3|sinc)
Spectrum interpolation type used when spectra are resampled. The choices are:

	nearest - nearest neighbor
	 linear - linear
	  poly3 - 3rd order polynomial
	  poly5 - 5th order polynomial
	spline3 - cubic spline
	   sinc - sinc function
dispaxis = 2
Default dispersion axis. The dispersion axis is 1 for dispersion running along image lines and 2 for dispersion running along image columns. If the image header parameter DISPAXIS is defined it has precedence over this parameter.
database = "database"
Database (directory) used for storing aperture and dispersion information.
verbose = no
Print verbose information available with various tasks.
logfile = "logfile", plotfile = ""
Text and plot log files. If a filename is not specified then no log is kept. The plot file contains IRAF graphics metacode which may be examined in various ways such as with gkimosaic .
records = ""
Dummy parameter to be ignored.
version = "KPNOCOUDE: ..."
Version of the package.


The following parameters are part of the params parameter set and define various algorithm parameters for do3fiber .


line = INDEF, nsum = 10
The dispersion line (line or column perpendicular to the dispersion axis) and number of adjacent lines (half before and half after unless at the end of the image) used in finding, recentering, resizing, editing, and tracing operations. A line of INDEF selects the middle of the image along the dispersion axis.
extras = no (apsum)
Include extra information in the output spectra? When cleaning or using variance weighting the cleaned and weighted spectra are recorded in the first 2D plane of a 3D image, the raw, simple sum spectra are recorded in the second plane, and the estimated sigmas are recorded in the third plane.


lower = -3., upper = 3. (apdefault)
Default lower and upper aperture limits relative to the aperture center. These limits are used when the apertures are first found and may be resized automatically or interactively.


ylevel = 0.(apresize)
Data level at which to set aperture limits during automatic resizing. It is a fraction of the peak relative to a local background.


t_step = (aptrace)
Step along the dispersion axis between determination of the spectrum positions. Note the nsum parameter is also used to enhance the signal-to-noise at each step.
t_function = "spline3", t_order = (aptrace)
Default trace fitting function and order. The fitting function types are "chebyshev" polynomial, "legendre" polynomial, "spline1" linear spline, and "spline3" cubic spline. The order refers to the number of terms in the polynomial functions or the number of spline pieces in the spline functions.
t_niterate = 1, t_low = 3., t_high = 3. (aptrace)
Default number of rejection iterations and rejection sigma thresholds.


buffer = 1. (apscatter)
Buffer distance from the aperture edges to be excluded in selecting the scattered light pixels to be used.
apscat= "" (apscatter)
Fitting parameters across the dispersion. This references an additional set of parameters for the ICFIT package. The default is the "apscat1" parameter set.
apscat= "" (apscatter)
Fitting parameters along the dispersion. This references an additional set of parameters for the ICFIT package. The default is the "apscat2" parameter set.


weights = "none" (apsum)
Type of extraction weighting. Note that if the clean parameter is set then the weights used are "variance" regardless of the weights specified by this parameter. The choices are:
The pixels are summed without weights except for partial pixels at the ends.
The extraction is weighted by the variance based on the data values and a poisson/ccd model using the gain and readnoise parameters.
pfit = "fit1d" (apsum) (fit1d|fit2d)
Profile fitting algorithm for cleaning and variance weighted extractions. The default is generally appropriate for most data but users may try the other algorithm. See approfiles for further information.
lsigma = 3., usigma = 3. (apsum)
Lower and upper rejection thresholds, given as a number of times the estimated sigma of a pixel, for cleaning.
nsubaps = (apsum)
During extraction it is possible to equally divide the apertures into this number of subapertures.


f_interactive = yes (fit1d)
Fit the composite one dimensional flat field spectrum interactively? This is used if fitflat is set and a two dimensional flat field spectrum is specified.
f_function = "spline3", f_order = (fit1d)
Function and order used to fit the composite one dimensional flat field spectrum. The functions are "legendre", "chebyshev", "spline1", and "spline3". The spline functions are linear and cubic splines with the order specifying the number of pieces.


threshold = 10. (autoidentify/identify/reidentify)
In order for a feature center to be determined the range of pixel intensities around the feature must exceed this threshold.
coordlist = "linelists$idhenear.dat" (autoidentify/identify)
Arc line list consisting of an ordered list of wavelengths. Some standard line lists are available in the directory "linelists$".
match = -3. (autoidentify/identify)
The maximum difference for a match between the dispersion function prediction value and a wavelength in the coordinate list.
fwidth = 3.(autoidentify/identify)
Approximate full base width (in pixels) of arc lines.
cradius = 4. (reidentify)
Radius from previous position to reidentify arc line.
i_function = "legendre", i_order = (autoidentify/identify)
The default function and order to be fit to the arc wavelengths as a function of the pixel coordinate. The functions choices are "chebyshev", "legendre", "spline1", or "spline3".
i_niterate = 3, i_low = 3.0, i_high = 3.(autoidentify/identify)
Number of rejection iterations and sigma thresholds for rejecting arc lines from the dispersion function fits.
refit = yes (reidentify)
Refit the dispersion function? If yes and there is more than 1 line and a dispersion function was defined in the arc reference then a new dispersion function of the same type as in the reference image is fit using the new pixel positions. Otherwise only a zero point shift is determined for the revised fitted coordinates without changing the form of the dispersion function.
addfeatures = no (reidentify)
Add new features from a line list during each reidentification? This option can be used to compensate for lost features from the reference solution. Care should be exercised that misidentified features are not introduced.


select = "interp" (refspectra)
Selection method for assigning wavelength calibration spectra. Note that an arc assignment table may be used to override the selection method and explicitly assign arc spectra to object spectra. The automatic selection methods are:
Average two reference spectra without regard to any sort parameter. If only one reference spectrum is specified then it is assigned with a warning. If more than two reference spectra are specified then only the first two are used and a warning is given. This option is used to assign two reference spectra, with equal weights, independent of any sorting parameter.
Select the nearest following spectrum in the reference list based on the sorting parameter. If there is no following spectrum use the nearest preceding spectrum.
Interpolate between the preceding and following spectra in the reference list based on the sorting parameter. If there is no preceding and following spectrum use the nearest spectrum. The interpolation is weighted by the relative distances of the sorting parameter.
Match each input spectrum with the reference spectrum list in order. This overrides the reference aperture check.
Select the nearest spectrum in the reference list based on the sorting parameter.
Select the nearest preceding spectrum in the reference list based on the sorting parameter. If there is no preceding spectrum use the nearest following spectrum.
sort = "jd", group = "ljd" (refspectra)
Image header keywords to be used as the sorting parameter for selection based on order and to group spectra. A null string, "", or the word "none" may be use to disable the sorting or grouping parameters. The sorting parameter must be numeric but otherwise may be anything. The grouping parameter may be a string or number and must simply be the same for all spectra within the same group (say a single night). Common sorting parameters are times or positions. In do3fiber the Julian date (JD) and the local Julian day number (LJD) at the middle of the exposure are automatically computed from the universal time at the beginning of the exposure and the exposure time. Also the parameter UTMIDDLE is computed.
time = no, timewrap = 17. (refspectra)
Is the sorting parameter a 24 hour time? If so then the time origin for the sorting is specified by the timewrap parameter. This time should precede the first observation and follow the last observation in a 24 hour cycle.


linearize = yes (dispcor)
Interpolate the spectra to a linear dispersion sampling? If yes the spectra will be interpolated to a linear or log linear sampling If no the nonlinear dispersion function(s) from the dispersion function database are assigned to the input image world coordinate system and the spectral data are not interpolated.
log = no (dispcor)
Use linear logarithmic wavelength coordinates? Linear logarithmic wavelength coordinates have wavelength intervals which are constant in the logarithm of the wavelength.
flux = yes (dispcor)
Conserve the total flux during interpolation? If no the output spectrum is interpolated from the input spectrum at each output wavelength coordinate. If yes the input spectrum is integrated over the extent of each output pixel. This is slower than simple interpolation.


The environment parameter imtype is used to determine the extension of the images to be processed and created. This allows use with any supported image extension. For STF images the extension has to be exact; for example "d1h".


The do3fiber reduction task is specialized for scattered light subtraction, extraction, flat fielding, and wavelength calibration of multifiber data in which some fibers are used to take object spectra and other fibers are used to take simultaneous arc spectra. A three fiber instrument of this type (one object and two arc fibers) is available at the KPNO coude feed. The default parameters are set for this configuration. If there are a large number of fibers and fiber throughput and sky fiber subtraction is needed the dofiber task should be used.

The do3fiber task is a command language script which collects and combines the functions and parameters of many general purpose tasks to provide a single complete data reduction path. The task provides a degree of guidance, automation, and record keeping necessary when dealing with this type of multifiber data.

The general organization of the task is to do the interactive setup steps first using representative calibration data and then perform the majority of the reductions automatically, and possibly as a background process, with reference to the setup data. In addition, the task determines which setup and processing operations have been completed in previous executions of the task and, contingent on the redo and update options, skip or repeat some or all the steps.

The description is divided into a quick usage outline followed by details of the parameters and algorithms. The usage outline is provided as a checklist and a refresher for those familiar with this task and the component tasks. It presents only the default or recommended usage. Since do3fiber combines many separate, general purpose tasks the description given here refers to these tasks and leaves some of the details to their help documentation.

Usage Outline

The images are first processed with ccdproc for overscan, bias, and dark corrections. The do3fibers task will abort if the image header keyword CCDPROC, which is added by ccdproc , is missing. If the data processed outside of the IRAF ccdred package then a dummy CCDPROC keyword should be added to the image headers; say with hedit .
Set the do3fiber parameters with eparam . Specify the object images to be processed, the flat field image as the aperture reference and the flat field, and one or more arc images. If there are many object or arc spectra per setup you might want to prepare "@ files".
Run the task. This may be repeated multiple times with different observations and the task will generally only do the setup steps once and only process new images. Queries presented during the execution for various interactive operations may be answered with "yes", "no", "YES", or "NO". The lower case responses apply just to that query while the upper case responses apply to all further such queries during the execution and no further queries of that type will be made.
The apertures are defined using the specified aperture reference image which is usually a flat field in which both the object and arc fibers are illuminated. The specified number of fibers are found automatically and sequential apertures assigned.
A query is given allowing the apertures to be interactively reviewed. In this mode one may adjust the aperture widths as desired either explicitly (:lower and :upper), with the cursor (l and u), at a particular flux level (y), or with an automatic algorithm (z) as described by apresize . To exit type q.
The fiber positions at a series of points along the dispersion are measured and a function is fit to these positions. This may be done interactively to adjust the fitting parameters. Not all fibers need be examined and the "NO" response will quit the interactive fitting. To exit the interactive fitting type q.
If scattered light subtraction is to be done the flat field image is used to define the scattered light fitting parameters interactively. If one is not specified then the aperture reference image is used for this purpose.

There are two queries for the interactive fitting. A graph of the data between the defined reference apertures separated by a specified buffer distance is first shown. The function order and type may be adjusted. After quiting with q the user has the option of changing the buffer value and returning to the fitting, changing the image line or column to check if the fit parameters are satisfactory at other points, or to quit and accept the fit parameters. After fitting all points across the dispersion another graph showing the scattered light from the individual fits is shown and the smoothing parameters along the dispersion may be adjusted. Upon quiting with q you have the option of checking other cuts parallel to the dispersion or quiting and finishing the scattered light function smoothing and subtraction.

If there is a throughput image then this is corrected for scattered light noninteractively using the previous fitting parameters.

If flat fielding is to be done the flat field spectra are extracted. The average spectrum over all fibers is determined and a function is fit interactively (exit with q). This function is generally of sufficiently high order that the overall shape is well fit. This function is then used to normalize the individual flat field spectra. The final response spectra are normalized to a unit mean over all fibers.
If dispersion correction is selected the first arc in the arc list is extracted. The middle fiber is used to identify the arc lines and define the dispersion function using the task autoidentify . The crval and cdelt parameters are used in the automatic identification. Whether or not the automatic identification is successful you will be shown the result of the arc line identification. If the automatic identification is not successful identify a few arc lines with m and use the l line list identification command to automatically add additional lines and fit the dispersion function. Check the quality of the dispersion function fit with f. When satisfied exit with q.
The remaining fibers are automatically reidentified. You have the option to review the line identifications and dispersion function for each fiber and interactively add or delete arc lines and change fitting parameters. This can be done selectively, such as when the reported RMS increases significantly.
If the spectra are to be resampled to a linear dispersion system (which will be the same for all spectra) default dispersion parameters are printed and you are allowed to adjust these as desired.
The object spectra are now automatically scattered light subtracted, extracted, flat fielded, and dispersion corrected. The reference apertures are first assigned to the object spectra. If the recenter option is set the apertures will have a shift applied based on recentering the fiber profiles. If the edit option is set you may review and modify the aperture definitions interactively. Any new arcs assigned to the object images are automatically extracted and dispersion functions determined. A zero point wavelength correction is computed from the arc fiber spectra and applied to the object spectrum.
The option to examine the final spectra with splot may be given. To exit type q.
If scattered light is subtracted from the input data a copy of the original image is made by appending "noscat" to the image name. If the data are reprocessed with the redo flag the original image will be used again to allow modification of the scattered light parameters.

The final spectra will have the same name as the original 2D images with a ".ms" extension added.

Spectra and Data Files

The basic input consists of multifiber object and calibration spectra stored as IRAF images. The type of image format is defined by the environment parameter imtype . Only images with that extension will be processed and created. There are two types of calibration images. These are flat fields and comparison lamp arc spectra. The raw CCD images must be processed to remove overscan, bias, and dark count effects. This is generally done using the ccdred package. The do3fiber task will abort if the image header keyword CCDPROC, which is added by ccdproc , is missing. If the data processed outside of the IRAF ccdred package then a dummy CCDPROC keyword should be added to the image headers; say with hedit . Flat fielding is generally not done at this stage but as part of do3fiber . If for some reason the flat field or calibration arc spectra have separate exposures through different fibers they may be simply added.

The assignment of arc calibration exposures to object exposures is generally done by selecting the nearest in time and interpolating. However, the optional arc assignment table may be used to explicitly assign arc images to specific objects. The format of this file is described in the task refspectra .

The final reduced spectra are recorded in one, two or three dimensional IRAF images. The images have the same name as the original images with an added ".ms" extension. Each line in the reduced image is a one dimensional spectrum with associated aperture, wavelength, and identification information. With a single object spectrum the image will be one dimensional and with multiple object spectra the image will be two dimensional. When the extras parameter is set the images will be three dimensional (regardless of the number of apertures) and the lines in the third dimension contain additional information (see apsum for further details). These spectral formats are accepted by the one dimensional spectroscopy tasks such as the plotting tasks splot and specplot .

Package Parameters

The kpnocoude package parameters set parameters affecting all the tasks in the package. Some of the parameters are not applicable to the do3fiber task. The observatory parameter is only required for data without an OBSERVAT header parameter (currently included in NOAO data). The spectrum interpolation type might be changed to "sinc" but with the cautions given in onedspec.package . The dispersion axis parameter is only needed if a DISPAXIS image header parameter is not defined. The other parameters define the standard I/O functions. The verbose parameter selects whether to print everything which goes into the log file on the terminal. It is useful for monitoring what the do3fiber task does. The log and plot files are useful for keeping a record of the processing. A log file is highly recommended. A plot file provides a record of apertures, traces, and extracted spectra but can become quite large. The plotfile is most conveniently viewed and printed with gkimosaic .

Processing Parameters

The input images are specified by image lists. The lists may be a list of explicit, comma separate image names, @ files, or image templates using pattern matching against file names in the directory. The aperture reference spectrum is used to find the spectrum profiles and trace them. Thus, this requires an image with good signal in all fibers which usually means a flat field spectrum. It is recommended that flat field correction be done using one dimensional extracted spectra rather than as two dimensional images. This is done if a flat field spectrum is specified. The arc assignment table is used to specifically assign arc spectra to particular object spectra and the format of the file is described in refspectra .

The detector read out noise and gain are used for cleaning and variance (optimal) extraction. The dispersion axis defines the wavelength direction of spectra in the image if not defined in the image header by the keyword DISPAXIS. The width parameter (in pixels) is used for the profile finding and centering algorithm (center1d ).

The number of fibers is fairly obvious. It is the number of fibers, including the arc fibers, to be automatically found and assigned apertures. The apertures are assigned aperture numbers sequentially. The object and arc fibers are identified by these aperture numbers as specified by the objaps and arcaps parameters. The defaults are for the case of three fibers in the sequence arc fiber, object fiber, and arc fiber.

The approximate central wavelength and dispersion are used for the automatic identification of the arc reference. They may be specified as image header keywords or values. The INDEF values search the entire range of the coordinate reference file but the automatic line identification algorithm works much better and faster if approximate values are given.

The next set of parameters select the processing steps and options. The scattered light option allows fitting and subtracting a scattered light surface from the input object and flat field. If there is significant scattered light which is not subtracted the fiber throughput correction will not be accurate. The flat fitting option allows fitting and removing the overall shape of the flat field spectra while preserving the pixel-to-pixel response corrections. This is useful for maintaining the approximate object count levels and not introducing the reciprocal of the flat field spectrum into the object spectra.

The apertures defined for the aperture reference image are assigned to each image. For the object images the apertures may be shifted across the dispersion by recentering the strongest profiles and averaging the individual shifts to form a single shift for all apertures. This corrects for shifts in the detector during the observations. The recenter parameter selects whether to apply this shift or not.

The edit option allows you to be queried to review the apertures assigned to each object image. If selected and the query answered affirmatively the apertures may be interactively shifted and resized. The query may also be answered with "NO" to turn off this option during processing. Note that the initial aperture definitions for the aperture reference image always allows editing.

The clean option invokes a profile fitting and deviant point rejection algorithm as well as a variance weighting of points in the aperture. These options require knowing the effective (i.e. accounting for any image combining) read out noise and gain. For a discussion of cleaning and variance weighted extraction see apvariance and approfiles .

The dispersion correction option selects whether to extract arc spectra, determine dispersion functions, assign them to the object spectra, and, possibly, resample the spectra to a linear (or log-linear) wavelength scale.

The splot option allows a query (which may be answered with "YES" or "NO" to eliminate the query) and then plotting of the final object spectra if answered affirmatively. The plotting is done with the task splot .

Generally once a spectrum has been processed it will not be reprocessed if specified as an input spectrum. However, changes to the underlying calibration data can cause such spectra to be reprocessed if the update flag is set. The changes which will cause an update are a new reference image, new flat field, and a new arc reference image. If all input spectra are to be processed regardless of previous processing the redo flag may be used. Note that reprocessing clobbers the previously processed output spectra.

The batch processing option allows object spectra to be processed as a background or batch job. This will only occur if the aperture editing and final spectrum plotting have been turned off, either with the task option parameter or by answering "NO" to the queries. The listonly option prints a summary of the processing steps which will be performed on the input spectra without actually doing anything. This is useful for verifying which spectra will be affected if the input list contains previously processed spectra. The listing does not include any arc spectra which may be extracted to dispersion calibrate an object spectrum.

The last parameter (excluding the task mode parameter) points to another parameter set for the algorithm parameters. The way do3fiber works this may not have any value and the parameter set params is always used. The algorithm parameters are discussed further in the next section.

Algorithms and Algorithm Parameters

This section summarizes the various algorithms used by the do3fiber task and the parameters which control and modify the algorithms. The algorithm parameters available to the user are collected in the parameter set params . These parameters are taken from the various general purpose tasks used by the do3fiber processing task. Additional information about these parameters and algorithms may be found in the help for the actual task executed. These tasks are identified in the parameter section listing in parenthesis. The aim of this parameter set organization is to collect all the algorithm parameters in one place separate from the processing parameters and include only those which are relevant for this type of data. The parameter values can be changed from the defaults by using the parameter editor,

	cl> epar params

or simple typing params . The parameter editor can also be entered when editing the do3fiber parameters by typing :e params or simply :e if positioned at the params parameter.

Aperture Definitions

The first operation is to define the extraction apertures, which include the aperture width and position dependence with wavelength, for the object and arc fibers. This is done on a reference spectrum which is usually a flat field taken through both fibers. Other spectra will inherit the reference apertures and may apply a correction for any shift of the orders across the dispersion. The reference apertures are defined only once unless the redo option is set.

The selected number of fibers are found automatically by selecting the highest peaks in a cut across the dispersion. Apertures are assigned with a limits set by the lower and upper parameter and numbered sequentially. A query is then given allowing the apertures to be reviewed interactively. If answered affirmatively a cut across the orders is shown with the apertures marked and an interactive aperture editing mode is entered (see apedit ). The main thing to be concerned about is that the aperture numbers agree with the objaps and arcaps definitions. The aperture numbers may be changed with the i or o keys. The apertures may also be resized from the default limits. To exit the background and aperture editing steps type q.

Next the positions of the fiber profiles at various points along the dispersion are measured and a "trace function" is fit. The user is asked whether to fit the trace function interactively. This is selected to adjust the fitting parameters such as function type and order. When interactively fitting a query is given for each aperture. After the first aperture one may skip reviewing the other traces by responding with "NO". Queries made by do3fiber generally may be answered with either lower case "yes" or "no" or with upper case "YES" or "NO". The upper case responses apply to all further queries and so are used to eliminate further queries of that kind.

The above steps are all performed using tasks from the apextract package and parameters from the params parameters. As a quick summary, the dispersion direction of the spectra are determined from the package dispaxis parameter if not defined in the image header. The default line or column for finding the orders and the number of image lines or columns to sum are set by the line and nsum parameters. A line of INDEF (the default) selects the middle of the image. The automatic finding algorithm is described for the task apfind and basically finds the strongest peaks. The tracing is done as described in aptrace and consists of stepping along the image using the specified t_step parameter. The function fitting uses the icfit commands with the other parameters from the tracing section.


The actual extraction of the spectra is done by summing across the fixed width apertures at each point along the dispersion. The default is to simply sum the pixels using partial pixels at the ends. There is an option to weight the sum based on a Poisson noise model using the readnoise and gain detector parameters. Note that if the clean option is selected the variance weighted extraction is used regardless of the weights parameter. The sigma thresholds for cleaning are also set in the params parameters.

The cleaning and variance weighting options require knowing the effective (i.e. accounting for any image combining) read out noise and gain. These numbers need to be adjusted if the image has been processed such that the intensity scale has a different origin (such as a background light subtraction) or scaling (such as caused by unnormalized flat fielding). For optimal extraction and cleaning to work it is recommended that a datamax value be determined for the data and the fitflat option be used. For further discussion of cleaning and variance weighted extraction see apvariance and approfiles as well as apsum .

Scattered Light Subtraction

Scattered light may be subtracted from the input two dimensional image as the first step. This is done using the algorithm described in apscatter . This can be important if there is significant scattered light since the flat field/throughput correction will otherwise be incorrect. The algorithm consists of fitting a function to the data outside the defined apertures by a specified buffer at each line or column across the dispersion. The function fitting parameters are the same at each line. Because the fitted functions are independent at each line or column a second set of one dimensional functions are fit parallel to the dispersion using the evaluated fit values from the cross-dispersion step. This produces a smooth scattered light surface which is finally subtracted from the input image. Again the function fitting parameters are the same at each line or column though they may be different than the parameters used to fit across the dispersion.

The first time the task is run with a particular flat field (or aperture reference image if no flat field is used) the scattered light fitting parameters are set interactively using that image. The interactive step selects a particular line or column upon which the fitting is done interactively with the icfit commands. A query is first issued which allows skipping this interactive stage. Note that the interactive fitting is only for defining the fitting functions and orders. When the graphical icfit fitting is exited (with q) there is a second prompt allowing you to change the buffer distance (in the first cross-dispersion stage) from the apertures, change the line/column, or finally quit.

The initial fitting parameters and the final set parameters are recorded in the apscat1 and apscat2 hidden parameter sets. These parameters are then used automatically for every subsequent image which is scattered light corrected.

The scattered light subtraction modifies the input 2D images. To preserve the original data a copy of the original image is made with the same root name and the word "noscat" appended. The scattered light subtracted images will have the header keyword "APSCATTE" which is how the task avoids repeating the scattered light subtraction during any reprocessing. However if the redo option is selected the scattered light subtraction will also be redone by first restoring the "noscat" images to the original input names.

Flat Field Correction

Flat field corrections may be made during the basic CCD processing; i.e. direct division by the two dimensional flat field observation. In that case do not specify a flat field spectrum; use the null string "". The do3fiber task provides an alternative flat field response correction based on division of the extracted object spectra by the extracted flat field spectra. A discussion of the theory and merits of flat fielding directly verses using the extracted spectra will not be made here. The do3fiber flat fielding algorithm is the recommended method for flat fielding since it works well and is not subject to the many problems involved in two dimensional flat fielding.

The first step is extraction of the flat field spectrum, if specified, using the reference apertures. Only one flat field is allowed so if multiple flat fields are required the data must be reduced in groups. If the fitflat option is selected (the default) the extracted flat field spectra are averaged together and a smooth function is fit. The default fitting function and order are given by the parameters f_function and f_order . If the parameter f_interactive is "yes" then the fitting is done interactively using the fit1d task which uses the icfit interactive fitting commands.

The fitted function is divided into the individual flat field spectra to remove the basic shape of the spectrum while maintaining the relative individual pixel responses and any fiber to fiber differences. This step avoids introducing the flat field spectrum shape into the object spectra and closely preserves the object counts.

The final step is to normalize the flat field spectra by the mean counts over all the fibers. This normalization step is simply to preserve the average counts of the extracted object and arc spectra after division by the response spectra.

Dispersion Correction

If dispersion correction is not selected, dispcor =no, then the object spectra are simply extracted. If it is selected the arc spectra are used to dispersion calibrate the object spectra. There are four steps involved; determining the dispersion functions relating pixel position to wavelength, assigning the appropriate dispersion functions to a particular observation, determining a zero point wavelength shift from the arc fibers to be applied to the object fiber dispersion functions, and either storing the nonlinear dispersion function in the image headers or resampling the spectra to evenly spaced pixels in wavelength.

The first arc spectrum in the arc list is used to define the reference dispersion solution. It is extracted using the reference aperture definitions. The interactive task autoidentify is used to automatically define the dispersion function in one fiber. Whether or not it is successful the user is presented with the interactive identification graph. The automatic identifications can be reviewed and a new solution or corrections to the automatic solution may be performed. The dispersion functions for the other fibers are then determined automatically by reference to the first fiber using the task reidentify . Except in batch mode a query is given allowing the reidentified arc spectra to be examined interactively with identify . This would normally be done only if the information about the reidentification printed on the terminal indicates a problem such as a large increase in the RMS. This query may be eliminated in the usual way.

The set of arc dispersion function parameters are from autoidentify and reidentify . The parameters define a line list for use in automatically assigning wavelengths to arc lines, a parameter controlling the width of the centering window (which should match the base line widths), the dispersion function type and order, parameters to exclude bad lines from function fits, and parameters defining whether to refit the dispersion function, as opposed to simply determining a zero point shift, and the addition of new lines from the line list when reidentifying additional arc spectra. The defaults should generally be adequate and the dispersion function fitting parameters may be altered interactively. One should consult the help for the two tasks for additional details of these parameters and the operation of autoidentify .

If resampling of the spectra is selected by the parameter linearize all the arc dispersion functions are combined to provide a default starting and ending wavelength and dispersion with the same number of pixels is determined and the user is queried for any changes. This linear dispersion system will be applied to all spectra so that all the final processed object spectra will have the same dispersion sampling.

Once the reference dispersion functions are defined other arc spectra are extracted as they are assign to the object spectra. The assignment of arcs is done either explicitly with an arc assignment table (parameter arctable ) or based on a header parameter such as a time. The assignments are made by the task refspectra . When two arcs are assigned to an object spectrum an interpolation is done between the two dispersion functions. This makes an approximate correction for steady drifts in the dispersion. Because the arc fibers monitor any zero point shifts in the dispersion functions, due to translation and rotation of the detector, it is probably only necessary to have one or two arc spectra, one at the beginning and/or one at the end of the night.

The tasks setjd and setairmass are automatically run on all spectra. This computes and adds the header parameters for the Julian date (JD), the local Julian day number (LJD), the universal time (UTMIDDLE), and the air mass at the middle of the exposure. The default arc assignment is to use the Julian date grouped by the local Julian day number. The grouping allows multiple nights of data to be correctly assigned at the same time.

When the object spectra are extracted so are the simultaneous arc spectra. A zero point shift of the arc spectra relative to the dispersion solutions of an assigned full arc observation is computed using reidentify . The zero point shifts from the arc fibers are then interpolated across the detector based on the positions of the arc apertures to the positions of the object apertures. A linear interpolation is used which accounts for a rotation of the detector as well as a translation along the dispersion. The interpolated zero point wavelength shifts are then added to the dispersion functions from the full arc observation for the object fibers. Note that this does not assume that the object and arc fiber dispersion functions are the same or have the same wavelength origin, but only that the interpolated shifts in wavelength zero point apply to all fibers. When there are two assigned full arc spectra the above steps are done independently and the final pair of zero point corrected dispersion functions for each object fiber are combined using the assigned weights. Once the dispersion function correction is determined from the extracted arc fiber spectra they are deleted leaving only the object spectra.

The last step of dispersion correction is setting the dispersion of the object spectra. There are two choices here. If the linearize parameter is not set the nonlinear dispersion functions are stored in the image header. Other IRAF tasks interpret this information when dispersion coordinates are needed for plotting or analysis. This has the advantage of not requiring the spectra to be interpolated and the disadvantage that the dispersion information is only understood by IRAF tasks and cannot be readily exported to other analysis software.

If the linearize parameter is set then the spectra are resampled to a linear dispersion relation either in wavelength or the log of the wavelength. The linear dispersion parameters are those defined previously for the arc reference image.

The linearization algorithm parameters allow selecting the interpolation function type, whether to conserve flux per pixel by integrating across the extent of the final pixel, and whether to linearize to equal linear or logarithmic intervals. The latter may be appropriate for radial velocity studies. The default is to use a fifth order polynomial for interpolation, to conserve flux, and to not use logarithmic wavelength bins. These parameters are described fully in the help for the task dispcor which performs the correction.


1. The following example uses artificial data and may be executed at the terminal (with IRAF V2.10). This is also the sequence performed by the test procedure "demos do3fiber".

kp> demos mkdo3fiber
Creating image demoobj ...
Creating image demoflat ...
Creating image demoarc ...
kp> do3fiber demoobj apref=demoflat flat=demoflat arcs=demoarc \
>>> width=4 edit=yes
Set reference apertures for demoflat
Resize apertures for demoflat?  (yes):
Edit apertures for demoflat?  (yes):
<Exit with 'q'>
Fit traced positions for demoflat interactively?  (yes):
Fit curve to aperture 1 of demoflat interactively  (yes):
<Exit with 'q'>
Fit curve to aperture 2 of demoflat interactively  (yes): N
Create response function
Extract flat field demoflat
Fit and ratio flat field demoflat
Create the normalized response ->  using bzero: 0.  and bscale: 1.
    mean: 1.  median: 1.034214  mode: 0.8378798
    upper: INDEF  lower: INDEF
Average aperture response:
1.  0.8394014
2.  1.034403
3.  1.126194
Extract arc reference image demoarc
Determine dispersion solution for demoarc
<Reset default line list with ":coord linelists$idhenear.dat">
<A dispersion solution is found automatically.>
<Examine the fit with 'f'>
<Exit fit with 'q' and exit task with 'q'>

REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Fri 11:04:32 06-Mar-92
  Reference image =, New image =, Refit = yes
     Image Data Found    Fit Pix Shift  User Shift  Z Shift     RMS - Ap 1   30/30  29/30  -0.00675       -0.04  -6.9E-6   0.252
Fit dispersion function interactively? (no|yes|NO|YES) (yes): n - Ap 3   30/30  29/30   -0.0154     -0.0928  -1.4E-5   0.303
Fit dispersion function interactively? (no|yes|NO|YES) (no): y
<Exit with 'q'> - Ap 3   30/30  29/30   -0.0154     -0.0928  -1.4E-5   0.303

Dispersion correct demoarc w1 = 5785.86, w2 = 7351.59, dw = 6.14, nw = 256
  Change wavelength coordinate assignments? (yes|no|NO): N
Extract object spectrum demoobj
Edit apertures for demoobj?  (yes): n
Assign arc spectra for demoobj
[demoobj] refspec1='demoarc'
Reidentify arc fibers in demoobj with respect to demoarc

REIDENTIFY: NOAO/IRAF V2.10BETA valdes@puppis Fri 11:04:52 06-Mar-92
  Reference image =, New image =, Refit = no
  Image Data   Found    Fit Pix Shift  User Shift  Z Shift     RMS - Ap 1  27/30  27/27   0.00502      0.0263  3.99E-6   0.175 - Ap 3  27/30  27/27   8.62E-4       0.006  5.07E-7   0.248
Dispersion correct demoobj REFSHFT1 = ' interp', shift = -0.0050,
rms = 0.00282813 intercept = -0.0118401, slope = 2.70764E-4 ap = 2, w1 = 5785.86, w2 = 7351.59, dw = 6.14, nw = 256
Splot spectrum? (no|yes|NO|YES) (yes):
<Exit with 'q'>


The initial arc line identifications is done with the automatic line identification algorithm.
DO3FIBER V2.10.3
The usual output WCS format is "equispec". The image format type to be processed is selected with the imtype environment parameter. The dispersion axis parameter is now a package parameter. Images will only be processed if the have the CCDPROC keyword. A datamax parameter has been added to help improve cosmic ray rejection. A scattered light subtraction processing option has been added.


apedit, apfind, approfiles, aprecenter, apresize, apsum, aptrace, apvariance, ccdred, center1d, dispcor, fit1d, icfit, identify, observatory, onedspec.package, refspectra, reidentify, setairmass, setjd

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