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Hi all,I've been having some problems with extracting some spectra lately and I'm looking for some help. Whenever I attempt to extract the spectra from the reduced data, I end up getting strange artifacts in many of them. Mostly, these tend to make the spectra look like a roller coaster, with bumps and dips across the spectra, though not all are affected.The strange part is that we're almost positive that the reduced 2d data is fine. Displaying the 2d image graphically shows nothing out of the ordinary that looks like it would cause this. Additionally, we tried a very, very rudimentary "extraction" by plotting the sum of the columns that contain the spectra minus the sum of some background columns, and even then the data looked fine, so we are convinced that it's simply a reduction problem.Also interesting was that the shape of the artifacts was highly sensitive to the fitting function for the aperture (which seemed very strange). Just changing the order or type of the function would change the shape of the artifacts in the final, 1d spectra dramatically, even though the RMS barely budged. Playing around with using different background regions didn't give much success either. The only luck we've had has been from changing the "profile fitting type" from fit1d to fit2d under the extraction parameters, which got rid of most of the problems (though not all), but we still can't figure out why this was the case.The data was taken using EMMI on the ESO 3.6m NTT, if that helps at all. I copied our apall parameters below. Thanks for any ideas you may have!Matt[code:1:4780dd1996]input = @complist List of input images
(output = ) List of output spectra
(apertur= ) Apertures
(format = onedspec) Extracted spectra format
(referen= ) List of aperture reference images
(profile= ) List of aperture profile images(interac= yes) Run task interactively?
(find = yes) Find apertures?
(recente= yes) Recenter apertures?
(resize = yes) Resize apertures?
(edit = yes) Edit apertures?
(trace = yes) Trace apertures?
(fittrac= yes) Fit the traced points interactively?
(extract= yes) Extract spectra?
(extras = yes) Extract sky, sigma, etc.?
(review = yes) Review extractions?(line = INDEF) Dispersion line
(nsum = 3) Number of dispersion lines to sum or median # DEFAULT APERTURE PARAMETERS(lower = -5.) Lower aperture limit relative to center
(upper = 5.) Upper aperture limit relative to center
(apidtab= ) Aperture ID table (optional) # DEFAULT BACKGROUND PARAMETERS(b_funct= chebyshev) Background function
(b_order= 2) Background function order
(b_sampl= -40:-20,20:40) Background sample regions
(b_naver= -3) Background average or median
(b_niter= 1) Background rejection iterations
(b_low_r= 3.) Background lower rejection sigma
(b_high_= 3.) Background upper rejection sigma
(b_grow = 0.) Background rejection growing radius # APERTURE CENTERING PARAMETERS(width = 5.) Profile centering width
(radius = 5.) Profile centering radius
(thresho= 0.) Detection threshold for profile centering # AUTOMATIC FINDING AND ORDERING PARAMETERSnfind = 1 Number of apertures to be found automatically
(minsep = 5.) Minimum separation between spectra
(maxsep = 1000.) Maximum separation between spectra
(order = increasing) Order of apertures # RECENTERING PARAMETERS
(aprecen= ) Apertures for recentering calculation
(npeaks = INDEF) Select brightest peaks
(shift = yes) Use average shift instead of recentering? # RESIZING PARAMETERS(llimit = INDEF) Lower aperture limit relative to center
(ulimit = INDEF) Upper aperture limit relative to center
(ylevel = 0.1) Fraction of peak or intensity for automatic width
(peak = yes) Is ylevel a fraction of the peak?
(bkg = yes) Subtract background in automatic width?
(r_grow = 0.) Grow limits by this factor
(avglimi= no) Average limits over all apertures? # TRACING PARAMETERS(t_nsum = 3) Number of dispersion lines to sum
(t_step = 3) Tracing step
(t_nlost= 5) Number of consecutive times profile is lost before quitting
(t_funct= legendre) Trace fitting function
(t_order= 3) Trace fitting function order
(t_sampl= *) Trace sample regions
(t_naver= 1) Trace average or median
(t_niter= 2) Trace rejection iterations
(t_low_r= 3.) Trace lower rejection sigma
(t_high_= 3.) Trace upper rejection sigma
(t_grow = 0.) Trace rejection growing radius # EXTRACTION PARAMETERS(backgro= fit) Background to subtract
(skybox = 1) Box car smoothing length for sky
(weights= none) Extraction weights (none|variance)
(pfit = fit1d) Profile fitting type (fit1d|fit2d)
(clean = yes) Detect and replace bad pixels?
(saturat= INDEF) Saturation level
(readnoi= 5.158) Read out noise sigma (photons)
(gain = 1.274) Photon gain (photons/data number)
(lsigma = 4.) Lower rejection threshold
(usigma = 4.) Upper rejection threshold
(nsubaps= 1) Number of subapertures per aperture
(mode = ql)
[/code:1:4780dd1996]

Hello Matt,A straight aperture extraction rarely has problems. I think you will find if you set [code:1:7fe0906479]weights=no, clean=no[/code:1:7fe0906479] that you will get a smoother spectrum.However, I assume you would like to use the clean option. Since this requires fitting a smooth profile to the data in order to compare the individual wavelength profiles to the model (this model is also needed for weighting) there are some things that can go wrong with the modeling. When this happens things can look very wrong because problems propagate over swaths of wavelength.One simple thing to fix is sensitivity to strong cosmic rays. By setting the saturation to something just above the range of the actual data (i.e. chopping off the tops of very strong spikes) things often work much better.The smoothing function used for fitting the profiles is largely hidden (except for the choice of pfit). The only implicit parameter is the order of the trace function. If the trace function needed/used is higher then it assumes the smoothing function has to be of a higher order.I hope this helps.Yours,
Frank Valdes