The data reduction package contains the tasks required to reduce the calibration and target data.
The first version of the data reduction package deals separately with the different types of data (eg dome flats, sky flats, arc lamps, flux standards and target observations. For each type of data there are one or more pipeline scripts to reduce the data. Each pipeline script runs a series of IRAF tasks. Each IRAF task can also run stand-alone.
PixCel outputs a FITS file for each read, which contains the four quadrants assembled into one image. An observation usually contains several reads. The first stage of the data reduction stacks all the required reads from one observation into a single multi-extension FITS file, performs cosmic ray rejection if required and outputs a multi-extension FITS file containing science, variance and data quality extensions. If required we then subtract a background image, and extract the spectra. The final data reduction product for most types of observation is a multi-extension FITS file containing the extracted spectra and the associated error and data quality information. This file also contains a table extension which provides the position on the sky for each extracted spectrum. This then allows us to reconstruct the image on the IFU in any subset of the observed wavelength range.
We use FITS header keywords to drive whether a task in a data reduction pipeline is performed or not. These keywords are initially set at the beginning of an observation with the instrument control software, but can also be easily changed during the data reduction process.
Below is an illustration of the order of the pipeline tasks that would be run to produce a QuickLook data reduction (ie not wavelength or flux calibrated) from a beamswitched pair.
FLOWCHART - gif postscript