The following pages contain full descriptions of the modules that are available in the MosaicGUI pipeline. For information on how to turn these modules on and off on the command line, see Chapter 9. For suggestions on which modules to use, see §2.5 Which Modules Should I Choose?
Module listing:
Initial Setup
Mosaic Settings
S/N Estimator
MedFilter
Detect Radhit
Fiducial Image Frame
Mosaic Geometry
Mosaic Interpolate
Detect (Outlier)
Mosaic Projection
Mosaic Coverage
Mosaic Dual Outlier
Level
Mosaic Outlier
Mosaic Box Outlier
Mosaic RMask
Mosaic Reinterpolate
Fix Coverage
Mosaic CoAdder
Mosaic Combine
Mosaic MedFilter
Create RMask Mosaic
Make Array Correction Files
Make Array Correction Mosaic
5.6.1 Mosaic Modules: Initial Setup
Command Line Equivalent: N/A
Default Output Directory: N/A
Depends On: None
PURPOSE
Set up the input and output files for the loaded flow.
INPUT
Image Stack File: 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.
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:
Sigma List File: The text file containing the list of uncertainty images that correspond to the input data files (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 input data images. 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. Usually this will be left blank, as the RMask images are created during the mosaicking process. This option allows you to specify a previously created list of RMask images as input on second and subsequent runs of the pipeline, to save having to re-generate them.
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 §5.6.4). This is an optional input file, as it is often generated from the input data using the Fiducial Image Frame module. 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).
COMMAND LINE INPUT
The following are set in the Global Parameters part of the namelist:
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 Overlap and Mosaic into your reduction flow, Overlap will use the Initial Settings files as input, but Mosaic will use the modified files output by Overlap). Only Input Image Stack and Output Directory are required, but Sigma File List, DCE Status Mask List and Pmask FITS File are recommended.
***NEW*** Note that with version 18.5.0 one can use multiprocessing to speed up MOPEX tasks. The tasks Overlap, Mosaic, Apex (Multi) and Apex User List (Multi) now allow multiprocessing of some steps. In the GUI, this is set in Initial Setup, Multi-Processing Mode. The options are "on", "off", and "manual". The default is "on" -- this grabs 3/4 of the available processors. Setting "manual" lets the user set the number of processors used. You should see speed-ups of at least 2x.
If using command-line, add these lines at the top of your namelist:
do_multiprocess = on | off | manual default = off
ncpu_multiprocess = 1 default = 1
If "manual" is set, set ncpu_multiprocess to the number of processors to use.
