3.2	Pipeline Processing Overview

The calibration pipeline, calcos, has been developed by the Space Telescope Science Institute (STScI) to support the calibration of HST/COS data. Although the COS pipeline benefits from the design heritage of previous HST instruments and of the Far Ultraviolet Spectroscopic Explorer (FUSE), the calcos modules are tailored specifically to the COS instrument and based on data reduction algorithms defined by the COS Instrument Definition Team (IDT). As with other HST pipelines, calcos uses an association table (the _asn files) to specify the data files to be included, and employs header keywords to specify the calibration steps to be performed and the reference files to be used. Calcos is written in Python, which enables the pipeline and users to take advantage of an extremely productive, open-source, easy-to-read scripting language, with many libraries for data reduction and analysis. Calcos is in the stsci_python package, which is available for download from STScI:

http://www.stsci.edu/institute/software_hardware/pyraf/current/download

Calcos is designed with a common underlying structure for processing FUV and NUV channels which, respectively, use a cross delay line (XDL) and a Multi Anode Microchannel Array (MAMA) detector. The calcos calibration pipeline includes pulse-height filtering and geometric correction for the FUV channel, and flat-field, deadtime, and Doppler correction for both channels. It includes methods for obtaining an accurate wavelength calibration by using the onboard spectral line lamps. A background subtracted spectrum is produced and the instrument sensitivity is applied to create the final flux calibrated spectrum.

There are two basic types of raw data files: TIME-TAG photon lists and ACCUM images of the detector. In general, calcos must convert these into one dimensional calibrated flux and wavelength arrays. Calcos must be able to perform different types of calibration processes to accommodate the different input types.

The level of calibration performed depends upon the data type.

•	Acquisition mode exposures (ACQ/search, ACQ/PEAKXD, and ACQ/PEAKD) are not calibrated by calcos, with the exception of ACQ/IMAGE. Only the raw data from these modes are provided.

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All other science data, including NUV imaging data (ACQ/IMAGE), are completely calibrated. This includes geometric and thermal correction for the FUV data, flat fielding, linearity corrections and pulse height filtering. The spectroscopic data are also flux calibrated and corrected for time dependence in the instrumental sensitivity. The data flow and calibration modules for processing the data are described in detail in sections 3.3 and 3.4.

•	Raw data taken in TIME-TAG mode are event lists (rawtag binary tables). The basic calibration is done on the tabular data, producing a calibrated (corrtag) events table. The events are then accumulated into a calibrated image (flt) by calcos.

•	Raw data taken in ACCUM mode (_rawaccum) are binned to an image array onboard the spacecraft.

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For spectral data, calcos extracts a spectrum from the flat-fielded image, computes associated wavelengths, and converts the count rates to flux densities, yielding a one-dimensional, background subtracted spectrum. For FUV data there will normally be two spectra, one from segment A and one from segment B. For NUV data there will normally be three spectra, one for each spectral “stripe”.

•	When multiple exposures comprise an observation, these are combined into a single, summed spectrum.

See Chapter 2 for the naming conventions of the various input, temporary, and output calibrated files.