Set up the input and output files for the loaded flow.
INPUT
Image Stack File: (Multiframe only) The text file containing the list of data files that you used as input into the APEX Multiframe pipeline. See Chapter 3 and Table 3.1 for more information on the input file requirements and format.
Mosaic File Name: (Single Frame only) The name of the single image that you used as input into the APEX Single Frame pipeline.
FIF File: (Single Frame only) The name of the FIF.tbl file that describes the input mosaic. This was either produced by the Mosaic pipeline and can be found in the output directory of the Mosaic run.
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 a 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 (see §6.5.5). This is the file called (by default) FIF.tbl, that was produced by either the Mosaic or APEX Multiframe pipeline. It can be found in the output directory of those runs.
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).
