The Spitzer IRS Custom Extraction, or SPICE, software provides a JAVA-based tool that allows the user to interactively extract Spitzer Infrared Spectrometer (IRS) spectra. The Spitzer automated pipeline provides default extractions, but many observing programs require further refinement to meet their science goals. For example, SPICE is designed to allow the user to:
Visualize the extraction performed by the Spitzer pipeline;
Examine features at known wavelengths in the 2D dispersed image;
Extract multiple targets along the slit;
Extract local sky spectra along the slit;
Re-extract target spectra after sky subtraction on the 2D dispersed image;
Re-extract target spectra after interpolation over e.g. bad pixels;
Overlay slit position, spectra from file, and line lists;
Perform custom extractions in Batch mode.
IRS spectra are not rectilinear on the array, and so spectral extraction requires careful tracing of the shape of each order. SPICE provides the tools to visualize the extraction window and properly perform the extraction. The software provided is the same as that used in the Spitzer pipeline, so consistent results may be obtained.
This manual serves as a brief introduction to both the SPICE interface and the Spitzer extraction pipeline. For a complete reference manual on IRS extraction, see the IRS Instrument Handbook.
1.1 Important Documentation
The following documents are recommended reading, and are referred to throughout this User’s Guide:
All Spitzer data must be downloaded from the Spitzer Heritage Archive (http://irsa.ipac.caltech.edu/applications/Spitzer/SHA/). You will be given a choice of data products to download. In general it is advised that the user download both the Basic Calibrated Data (BCD) and Post-BCD data. While the Post-BCD products will be suitable for many applications, they have been highly processed. The BCD products are necessary for anyone wishing to carry out their own spectrum extraction, and are the usual input files for SPICE. They can also provide a sanity check in assessing the reality of unusual features seen in the Post-BCD products.
The most commonly useful products available from the archive are the files with the following suffixes: *bcd.fits, *bmask.fits, *func.fits (individual BCDs, found in the bcd/ directory after downloading); *coad2.fits, *c2msk.fits, *c2unc.fits (co-added BCDs, found in the postbcd/ directory after downloading); *bksub.fits, *bkmsk.fits, *bkunc.fits (nod-subtracted observations, available for low-resolution staring AORs and found in the postbcd/ directory). A description of all of these products is available in the IRS Instrument Handbook.
1.2.3 Running SPICE - a walkthrough
When the GUI is started, the user is presented with a blank screen. To begin using SPICE an extraction flow must be initiated. SPICE flows are initiated using standard templates (point source, extended source, etc,) accessible from the File Menu. Extractions may be performed either upon single exposures by starting from a single BCD frame, or in batch mode for processing of many exposures. To get started, select File >Open SPICE generic template or File > Open Batch SPICE generic template. We begin here by describing the extraction of a spectrum from a single BCD.
A droplist menu will appear with the following three options:
Point Source with Regular Extract;
Point Source with Optimal Extract;
Extended Source with Regular Extract.
Select one of the flows and click the OK button. SPICE will set up the desired processing flow. Default parameters will be used initially, but may be modified by the user. To begin, specify the input files and output directory in Initialize Parameters and Files (§2.1). SPICE will attempt to match the uncertainty and pixel status bitmask files (§1.5, §1.6) to the input BCD based upon the standard naming convention. SPICE will automatically find the appropriate default calibration files for the input BCD.
Once the initial setup is complete, the user may specify custom parameters in any of the four SPICE modules (Chapter 2). New users may wish to begin by reading the overview of IRS pipeline processing (§1.3). The results of each module can be displayed in either the Plot or FITS windows (§1.7).
Processing flows can be saved using the File > Save and File >Save As options. They can be read back into SPICE later using File >Read SPICE user-saved Template (or File > Read Batch SPICE user-saved Template). FITS window images can be saved or printed from the File Menu, while spatial profiles or extracted spectra can be saved or printed from the right-click menu in the Plot window.
