Set up the input and output files for the loaded flow.
INPUT
Image Stack File: (Multiframe pipelines) The text file containing the list of input data files for the pipeline. Typically these are the *bcd.fits files that you download from the Spitzer data archive. See Chapter 3 and Table 3.1 for more information on the input file requirements and format.
Input File Name: (Single Frame pipelines) The name of the single image that you wish to use as input. For Spitzer data, this is usually the mosaic.fits file output by the Mosaic pipeline.
Sigma File Name: (Single Frame pipelines) The name of the uncertainty file that corresponds to the Input File Name. This is usually the mosaic_unc.fits file output by the Mosaic pipeline.
Coverage Map: (Single Frame pipelines) The name of the coverage map file that corresponds to the Input File Name. This is usually the mosaic_cov.fits file output by the Mosaic pipeline.
Output Directory: The directory that you want to set as your output directory for this run.
Multi-processing Mode: Switch to use multi-processing. See Discussion.
Processors for Multi-processing: Number of processors to use. See Discussion.
Optional Input and Mask Files: (Multiframe Pipelines only)
Sigma List File: The text file containing the list of uncertainty images that correspond to the files listed in Image Stack File (usually the *bunc.fits files; see Table 3.1 for more information).
DCE Status Mask List: The text file containing the list of mask images that flag temporarily-bad pixels in the files listed in Image Stack File. There should be a mask file for each of the input data files (these depend on the instrument, but will be labeled something like *msk.fits; see Table 3.1 for more information).
Fatal Mask Bit Pattern: This is the bit pattern that defines which type of flagged problems that you wish to set as fatal when combining the input images. See §8.11 for more information. There is a separate Fatal Bit Pattern for each type of mask that is being used as input (i.e. for the DCE Status masks, the RMasks and the PMask).
Rmask List File: The text file containing a list of outlier mask images. This option allows you to specify list of RMask images (e.g. those created by the Mosaic pipeline) to reject pixels in the input images that have been identified as outliers.
Pmask FITS File: The permanently-damaged pixel mask for the detector. This is a single FITS image, flagging the permanently damaged pixels in the instrument arrays. These files are stored in the <mopex_dir>/cal/ directory. There is a single PMask for each of the MIPS and IRS channels, but the IRAC ones have changed with time. See the file <mopex_dir>/pmasks.README for information on which PMask is applicable to your data. Note that the date that the data were taken is given in the DATE_OBS header keyword (not DATE - this is the date the file was written).
FIF file: The Fiducial Image Frame file. This is an optional input file, as it is often generated from the input data using the Fiducial Image Frame module, or taken from a previous pipeline (e.g. Mosaic). There are, however, a number of cases in which you might wish to use a user-specified FIF (e.g. if you are trying to match the field of view to the other data channels).
Verbose, NICE and save_namelist are only available on the command line. See §9.4.2.3 for more information.
OUTPUT
None
DISCUSSION
This module sets up the input files and top-level output directory for the first pipeline in the flow. Subsequent pipelines that have been inserted into the flow will use the output from the previous one (i.e. if you have inserted Mosaic and APEX into your reduction flow, Mosaic will use the Initial Settings files as input, but APEX will use the modified files output by Mosaic).
