MOPEX requires three main input types in order to carry out any processsing. The following section provides more information about each of the input types:
Input FITS images. These include the data images, the associated mask and uncertainty files and any calibration files.
Text files listing the input images. These should be in ASCII format.
The namelist. This is a parameter file specifying all of the input parameters to be used by MOPEX. This is usually built up from within the GUI, either from an empty flow, or by modifying existing templates, but you can also read in a previously-saved namelist from an ASCII file.
3.1 MOPEX Input Images
Images input into MOPEX do not have to be Spitzer data, but they do have to be in FITS format, with the standard FITS and WCS keywords. This software cannot process data cubes. The following keywords are required in the headers of the input files for the software to work: BITPIX, NAXIS, NAXIS1, NAXIS2, CRVAL1, CRVAL2, CRPIX1, CRPIX2, CTYPE1, CTYPE2. CD-Matrix elements or/and CDELT1, CDELT2, CROTA2 should be also present.
All of the projections in the WCS library are implemented, including "SIN", "TAN", "ZEA" (Lambert's zenith equal-area), "ARC" (zenith equidistant), and "STR" (stereographic). "TAN" is the default.
There are no practical restrictions on the size of the area of sky covered by the set of images in order to be processed by the mosaicker. The only nominal restriction is that the set of images should only cover one hemisphere (a solid angle < 2π Sr).
3.1.1 Spitzer Image Files
When you download your Spitzer data from the archive, you will find that there are many different files that are associated with each observation. Moreover, the filenames differ depending on the instruments. There are three types of image file that are commonly used as input into MOPEX: Basic Calibrated Data (BCD) images, the associated uncertainty image, and the associated bad pixel mask. See Table 3.1 for the recommended filenames for each instrument.
3.1.2 Additional Mask Files
In addition to the Status Mask Files that come with your Spitzer data (which flag the temporary bad pixels in each frame) there are two other types of mask file that can be input into MOPEX. The first is the mask of permanently damaged pixels (PMask). The PMasks for the IRAC instrument are updated every few months, depending on solar activity. They can be found in the <mopex_dir>/cal directory, or on the Spitzer website. The applicable PMask depends on the observation date of your data - check your FITS headers for the keyword DATE_OBS (not DATE, which is the date the file was written). See the pmasks.README file in the PMasks directory for the date range for which each PMask should be applied. PMasks for the MIPS instrument are updated less often.
The final set of images that can be input into MOPEX are RMask files, which are masks of pixels rejected as outliers in each frame. Typically, the user will generate RMasks as a product of outlier rejection during mosaicking (see §8.2), so they are not provided as input. However, it is possible to use RMasks as input, either from an earlier reduction, or from the automated Spitzer pipelines (which use MOPEX). They can also be specified as input into APEX Multiframe to ensure that outlier-rejected pixels are not used when running the PRF fitting on the individual BCDs.
Table 3.1: BCD data, uncertainty and mask filenames for each instrument
Instrument
Default BCD
BCD Uncertainties
DCE Status Mask
IRAC
bcd.fits or cbcd.fits
bunc.fits or cbunc.fits
bimsk.fits
IRS PU-16
bcdb.fits
uncb.fits
mskb.fits
IRS PU-22
bcdr.fits
uncr.fits
mskr.fits
MIPS-24
bcd.fits
bunc.fits
bbmsk.fits
MIPS-Ge (70 & 160)
bcd.fits or fbcd.fits
bunc.fits
bmask.fits
3.2 MOPEX Input List Files
The data, uncertainty, status mask and, possibly, the outlier mask image files are input into MOPEX via ASCII text files, containing one image filename per line. You will need to make a separate list file for each of the input image types, and the filenames must be in the same order in each of the input lists (i.e. the first filename in the list of image files must correspond to the first filename in the list of uncertainty files and the list of status mask files). As a rule, we recommend always including the full path name of the image files in the input lists e.g., the list of data files, InputImageList.txt, should look something like this:
As an example, to create the input lists for IRAC channel 1 data, in Unix (Solaris/Linux/Mac), you could use the following syntax:
unix% ls /<data_dir>/*bcd.fits > InputImageList.txt
unix% ls /<data_dir>/*bunc.fits > InputUncList.txt
unix% ls /<data_dir>/*bimsk.fits > InputMskList.txt
The input lists are specified in the Initial Setup module. The input file format is identical for both the command-line and the GUI interfaces.
The default location for the input files is in <working_dir>. When specifying input files, you should use either the full path name or the path relative to the working directory.
For more information on the User List point source input file for use with APEX User List and APEX User List Single Frame, see §8.10
3.3 MOPEX Input Namelist
The namelist files for each of the MOPEX pipelines contain all of the information about the modules and parameters to be used in a particular reduction. The ASCII versions of the template namelists used by MOPEX are all stored in the directory <mopex_dir>/cdf/. When using the GUI, you will most likely start from one of the included MOPEX template namelists (go to e.g. File > New Mosaic Pipeline to access the templates), and edit the included modules and parameters before running your reduction. Alternatively, you can choose to build up your namelist from an empty pipeline by going to File > New Empty MOPEX Pipeline.
Namelists can be written out to an ASCII file to save them for a later GUI reduction (File > Save As), or exported to command-line format to run them on the command line (File > Export Inner Pipeline), and namelists that have been set up on the command line (see Chapter 9) can be imported into the GUI and run there (File > Read Name List; this is valid for reading in both command-line and GUI namelists).
The names of some of the parameters on the command line have been changed in the GUI to improve clarity. You can find a full list of all the input parameters for the GUI, along with the command-line counterparts, in the MOPEX glossary pages, linked from the MOPEX webpage. For more information on the structure of the saved ASCII file namelist and running MOPEX on the command line, see Chapter 9.
