Data Reduction Frequently Asked Questions
I see small dark and bright regions in my normalized flat field - why?
These features are caused by straylight from 0th order light in adjacent slitlets. By default the pipeline normalizes the flat fields only along the dispersion axis using a flat field "spectrum" collapsed along the slit. The slit illumination instead is kept (sradius = -1), so that it is present to correct the slit illumination of the science data.
If an adjacent slit has its 0th order within the valid wavelength range of the slit being normalized, the stray light from this 0th order peak creates a strong local gradient in the flat field of the slit being normalized. The collapsed flat field "spectrum" contains an averaged value of this gradient, which then creates a hole/peak combination in the normalized flat field. This in turn creates a peak/hole combination in the flat-fielded science data.
The science data will also be contaminated by the 0th order light, but in a different way as the flat field spectra are all from one source while the science spectra are created by different sources.
This effect can be reduced by setting sradius > 0. In this case the spatial profile is determined by smoothing along the slit, row by row, which corrects most of the effect, but also removes the general slit illumination profile.