Algorithm and Function List

This package implements steps 3 through 8 of Horne's algorithm. The user is responsible for steps 1 and 2. The steps and implementation follow.
  • Step 1: Initial image processing - The user is responsible. This would include any sky subtraction or preprocessing. The package also requires the user to estimate the start and end x coordinate of the star's profile.
  • Step 2: Initial variance estimates - The user is responsible. Horne suggests (Reduced data)/Gain + (RMS read noise)^2. To further estimate the variance the package needs to know the readnoise and gain of the array. Also any preprocessing steps that add or reduce noise in the data need to be included in skyvar, which will be added to every varaince estimation.
  • Step 3: Fit sky background - fitbg.pro. Before an accurate profile can be estimated any remaining background bias must be subtracted off. This function fits the background outside the horizontal extraction boundaries at each wavelength in the data. It runs procvect.pro on each wavelength using the initial variance estimates as weights. It creates its own mask of bad pixels, using the user input mask as a start.
  • Step 4: Extract standard spectrum - stdspec.pro. Sums each background-subtracted wavelength within the bounds.
  • Step 5: Construct spatial profile.
  • Step 6: Revise variance estimates - fitprof.pro. Initially creates the spatial profile by (reduced - background) / (standard spectrum) Then uses procvect.pro on each column (which uses a sigma rejection scheme) with variance / spectrum^2 as weights. The user can select to fit a polynomial to each column, a running average to each colum, or a Gaussian to each row. The polynomial fit is default and the degree of fit can be user-defined. A degree of 3 is default. The running average fit actually uses a median filter when identifying bad pixels, then calculates a running average to return a profile. The Gaussian fit is a single dimension Gaussian, so any background geometry not identified by the background fitting will be problematic. All values are then made positive, and each wavelength is normalized to 1.
  • Step 7: Mask cosmic ray hits. - Done at every stage
  • Step 8: Extract optimal spectrum. - extrspec.pro After a profile and background (assumed to be perfect) are found extraction can occur. For each wavelength the spectrum is extracted and bad pixels are rejected using procvect, iterating until no bad pixels are found. The optimal extraction achieves the highest possible signal to noise ratio by weighting the pixels proportional to the profile divided by the variance.
  • Step 9: Iteration - The iteration scheme we used is suggested by Horne. Iterate 3 by itself to find cosmic rays in the background section. Iterate 5 and 6 to find the spatial profile image, but do not use the bad pixel mask found in step 5 for the extraction. Rather, next iterate 6, 7, and 8 to mask cosmic rays and optimally extract the spectrum.

    Functions in the package:

    The optimal extraction package: 
    DRIVER                            optspecextr.pro
                                 main driver routine
                                          |
                       --------------------------------------
                       |                  |                 |
VECTOR              fitbg.pro        fitprof.pro       extrspec.pro
SETUP          background fiting    profile fitting   spectrum extraction
                       |                  |                 |
                       --------------------------------------
                                          |
VECTOR                               procvect.pro
FITTING DRIVER                   bad pixel rejection
                                          |
                 -------------------------------------------------
                 |              |                |               |
VECTOR     polyfunc.pro   boxcarfunc.pro   gaussfunc.pro   extractspec.pro
FITTING     polynomial    running average    Gaussian    spectrum extraction
    The included adjustment functions: 
                                      adjgauss.pro
                                 driver routine
                                        |
                   ---------------------------------------
                   |                                     |
              findshift.pro                        sampleshift.pro
             center and width                   geometry modification
                   |      
           ----------------------
           |                    |
      centermass.pro         procvect.pro
       finds center      bad pixel rejection
                                |
                         gaussfunc.pro
                          Gaussian fit
  • Optspecextr.pro: Main driver routine. Gets the background frame from fitbg, the standard spectrum from stdextr, the profile frame from fitprof and the optimal spectrum from extrspec.

  • Fitbg.pro: Sends the data at each wavelength (row) to procvect.pro, using a polynomial fit and ignoring the data within the object limits. The resulting background fit is evaluated and subtracted from the input data.

  • Fitprof.pro: Driver for spatial profile fitting. The user may choose either a polynomial fit or a boxcar average along the spectral direction or a Gaussian fit along the spatial direction. The routine sets up the calculation and calls procvect.pro on each vector in the data, building a 2D frame with the results. If the spectrum trace is curved more by more than 2 pixels or if it changes quickly, the data can be expanded and shifted prior to profile estimation by a user set function. Adjgauss.pro is included in the package for this purpose.

  • Stdextr.pro: Calculates standard extraction, totaling each row within the spectrum bounds.

  • Extrspec.pro: Runs procvect.pro on each row of constant wavelength, which optimally estimates the spectrum amplitude at that point and calculates the variance.

  • Summaryopt.pro: Sends summary information to the screen for the user.

  • Procvect.pro: Iteratively fits a function to a linear array, removing up to one extreme pixel per iteration until none are found. It begins by either fitting the non-masked data or optimally extracting the spectrum and subtracting the result from the input data. The pixel with the largest residual (if it exceeds THRESH) is masked (marked as bad), and variances are recalculated. The process repeats with the original data and the new mask until no bad pixels are found. Finally, either the fit is evaluated at all values and returned or a final extraction is returned.

    Functions ending in "func" may be given to procvect as an argument.

  • Polyfunc.pro: Fits a polynomial of specified degree to the data vector divided by spectrum weighted inversely to the variance.

  • Gaussfunc.pro: Fits a Gaussian to the data / spectrum weighted inversely to the variance. If a Gaussian does not accuratly describe the data (because of a ray), if will try to fit it to median filtered data.

  • Extractfunc.pro: Optimally extracts the spectrum at that row.

  • Boxcarfunc.pro: Returns data / spectrum with a median filter when searching for cosmic rays, then returns a running average to the data when all the bad pixels have been eliminated.

  • Centermass.pro: Returns the center of mass for the data vector over the spectrum vector.

  • Adjguass.pro: Given a stack of data frames and the optimal extraction info, shifts and expands the input frames so that the centers of the profile (and optionally widths) of the profile line up.

  • Findshift.pro: Finds the center of the profile for each row in the data frame.

  • Sampleshift.pro: Given a data frame and a coresponding in coordiante array, returns a data frame corespoding to the out coordinate array, formed from the in data frame.

  • In.pro: Trivial function to test if an element is in an array

  • Keyword_defined.pro: Trivial function to see in a variable is defined.

  • Polyeval.pro: Evaluates polynomial coefficents

  • Testoptextr.pro: Tests the installation of the package. (Useful as example.)