Prepare Image:

    Load image from disk

    Subtract overscan and trim & assemble

Initial ISR Step

    Load the dark by filename

    Scale the dark by exposure time and subtract

        (you don not want to see the details of this!)

Source extraction (using SExtractor):

    Find the objects and centroids

Load SExtractor catalog

Process catalog to find the primary object

    return the x,y of the brightest, roundest object's centroid

Calculate the spectrum's bounding box, depending on dispersion direction and the order used

    Dispersion direction is either just x or y, not arbitrary angles yet

    Will need extending for arbitrary angles

Secondary ISR:

    Load masks from disk if masking

    removal of periodic pattern on chip

    Create initial dispersion relation

    Apply initial flatfielding

    Find and interpolate over cosmics

Extraction (choice between three methods:)

    Spectral extraction method 1:

        Calculate row-wise mean and sigma of background and subtract

        Row-wise, calculate:

            aperture flux

            PSF 1D-Gaussian flux

            Moffat flux

            Gauss-Moffat Flux

            Voigt flux

    Spectral extraction method 2:

        Calculate row-wise sum for aperture flux without subtracting background)

        Fit 1D Gaus for PSF flux (again, without bgSub, and without pedestal in fit function)

        Same for Voigt fit (no bgSub here either)

    Spectral extraction method 3 (two pass method):

        1st pass: fixed aperture, no centroid, meaning that:

            Per row:

                Fit 1D Gaus for PSF flux (again, without bgSub, and without pedestal in fit function)

        Between passes, fit the row-wise Gaussian's parameters with linear and quadratics functions describing the position and width of them as a function of row number i.e. position in the spectrum, respectively

        2nd pass: applying a variable aperture, using the 1D centroid and 1D sigma provided, meaning that:

            Per row:

                Regular aperture flux summing (still without bgSub I think)

                    aperture is centered at the row's centroid, and 6 sigma around it

                fit Gaussian over a very narrow range (120-180 pixels) up spectrum

Post-extraction:

Reflatfield

Find lines in spectrum

Match to known lines

Refine the dispersion relation calculation