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  1. Data Management
  2. DM-16699

Initial atmospec development work



    • Type: Story
    • Status: Done
    • Resolution: Done
    • Fix Version/s: None
    • Component/s: atmospec
    • Labels:


      Write a hacky, zeroth order version of the pipeline so that we have some skeleton tasks and structures in place to iterate on.

      This should probably be done on a user branch, but I wanted to have a ticket number for this work to save git hassles later on as this will touch more than just atmospec.

      This will initially be pretty hacky in places and probably not adhere to all standards, but will be tidied up before review.


      Checklist/to-do list/steps in Augustin's pipeline:


      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
      Find lines in spectrum
      Match to known lines
      Refine the dispersion relation calculation




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              mfisherlevine Merlin Fisher-Levine
              mfisherlevine Merlin Fisher-Levine
              John Swinbank, Merlin Fisher-Levine
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