It is highly likely that when you reduce your Spitzer data, you will include at least one set of mask files as input into the pipeline. The pixels in the mask files all contain coded information, or "bit definitions", depending on the status of a particular pixel. For example, a pixel with bit 10 flagged in the IRAC channel 1 PMask file indicates that that particular pixel in the IRAC channel 1 array has an excessive dark current that will affect all observations, while bit 14 indicates that the pixel is dead. For a full list of bit definitions, see the IRAC and MIPS Instrument Handbooks. When running MOPEX, you need to decide which of these codes you wish to set as "fatal", i.e. which of the flagged problems you consider so bad that the corresponding pixel in your data frame should be discarded. This is done by specifying a "Fatal Mask Bit Pattern" for each mask type, in the Initial Setup module. On the command line, the Fatal Bit Patterns are set in the general settings part of the namelist. The Fatal Mask Bit Patterns are calculated as follows:
Fatal Bit Pattern = 2(value of 1st required fatal bit) + 2(value of 2nd fatal bit) + .... + 2(value of nth fatal bit)
e.g. if you wished to set bits 7, 8, 9, 10 and 14 as fatal for your IRAC PMask file then you would set your PMask Fatal Mask Bit Pattern (PMask_Fatal_BitPattern in namelists) to: (27 + 28 + 29 + 210 + 214) = 18304. On the command line, you would include the following line in your namelist:
PMask_Fatal_BitPattern = 18304
The Fatal Bit Patterns for the other mask files can be set in the command-line namelists with the keywords:
DCE_Status_Mask_Fatal_BitPattern
RMask_Fatal_BitPattern
The currently recommended Fatal Mask Bit Patterns for each instrument are listed in the GUI templates.
