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COS Data Handbook 2.00
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COS Data Handbook > Chapter 5: COS Data Analysis > 5.1 Data Reduction and Analysis Applications

Most of the software tools for operating on COS FITS files are contained in two STSDAS packages:
hst_calib.hstcos: Contains COS specific tasks to calibrate and interpret data, including calcos. Many of these tasks are described in Chapter 3. A complete listing is presented in Section 5.1.1.
toolbox.ttools: Contains tasks to read and operate on FITS tables, which is the format used for COS spectral extractions, TIME-TAG data, and most COS reference files. These tasks and their syntax are described in Section 2.2.2 of the Introduction to HST Data Handbooks. We give specific examples of their use here in Section 5.1.2.
In addition to the above packages, most basic image manipulation software (e.g., display, daophot, imexamine, contour) and spectral analysis software (e.g., splot, tables, specfit, igi) available in PyRAF/IRAF/STSDAS can be used on COS data, either directly through the PyRAF or IRAF FITS interface or by converting data to another format. Chapter 3 of the Introduction to HST Data Handbooks includes information about how to display COS images and extracted spectra, as well as how and when to convert data formats, and a description of spectral analysis tasks. We present a brief summary of spectral display and analysis tasks in Section 5.1.3.
5.1.1 COS-Specific STSDAS Tasks
In Chapter 3, we gave detailed discussions of the use of the data reduction pipeline calcos. This task is contained in the STSDAS package hst_calib.hstcos. Other tasks useful for reducing and analyzing COS data are contained in this package as well. A complete listing and brief description of these tasks is given in Table 5.1. All of these tasks can be run in PyRAF. Consult the on-line help for each task for more information. Some of these tasks will be discussed in greater detail in the remainder of this chapter.
Table 5.1: COS-Specific Tasks
calcos tasks
For the most up-to-date list of COS specific tasks as well as examples please refer to the COS Instrument Web site:
5.1.2 FITS Table Tasks
COS spectral extractions, TIME-TAG data, and most COS reference files are stored in FITS tables. (See Section 2.4.1 for a description of the structure of the table extension files for spectral extractions and TIME-TAG data.) Tasks designed to handle this format can be used to examine and extract information from the tables. Here we give specific examples of the use of routines in ttools to help you get started. A sample output is given after each command.
To find out what information is given in the columns of a FITS table (the parameters listed here are discussed in depth in Section 5.4) using the tlcol task:
To use tread to look at the contents of the table:
Note that the number of columns displayed is limited by the width of the window that you are working in. To see more columns, you can start PyRAF or IRAF in a wider window or populate the task parameter columns in tread with some of the column names reported by tlcol:
The tlcol output indicates that some of the columns contain arrays of 16384 elements rather than a single value. For those columns, tread displays the value of the first element in the array. e.g., the initial wavelength in this x1d extraction is 1585.58 Angstroms. To plot an entire array, or plot one array against another, you can use a routine that operates on the table data directly:
You may want to change the parameter values in the supporting parameter sets axispar, dvpar, and pltpar to adjust the plotting. Alternatively, you may find it easier to work with FITS images. To make FITS image files of the arrays:
The images can then be displayed or operated on with standard FITS image handling routines such as python or IDL, e.g.:
Reference file FITS tables generally have many rows, with each row characterizing a specific operating mode, location on the detector, value of a parameter to be used in the reduction, etc.:
5.1.3 General Spectral Display and Analysis Tasks
Table 5.2 lists some of the more useful PyRAF/IRAF/STSDAS applications for displaying and analyzing COS spectral data.
Table 5.2: Spectral Analysis Tasks
ASCII tables
Some of the tasks are intended for browsing data or producing publication quality plots: the igi and sgraph tasks are described in Chapter 3 of the Introduction to HST Data Handbooks.
Specfit is a powerful spectral fitting routine that provides the user with many options for modelling emission and absorption features, continuum, and extinction. The fitting parameters can be linked to each other (e.g., fixed wavelength ratio or fixed flux ratio for two emission lines) and constrained. Different algorithms can be selected to first explore chi-square space, then rapidly achieve convergence in the deepest minimum. The application is fully described in a help file.
Plotting COS Spectral Images (flt)
The FUV data consists of separate files for each of the two FUV detector segments, segment A and segment B. In general, each segment contains one target spectrum and one wavecal. But, for the NUV data there are three disjoint portions of the spectrum present on the image for both the target and the wavecal. The following examples illustrate the use of the sgraph task to plot COS FUV and NUV spectra from the 2-D flt files.
Plotting COS Tabular Spectra (x1d)
COS spectra in tabular format are very similar to STIS spectra. The following examples illustrate the use of the sgraph task to plot COS FUV and NUV tabular spectra using a row selector and specifying the columns (e.g., wavelength and flux) to plot.

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