MOPEX Online Manual

Overlap Namelist Options

A: Input/Output Files

The following input filenames can be set within the namelist rather than having to specify them on the command line each time you run Overlap. See MOPEX Input Files for a description and the format of the input files, and see MOPEX Input Namelist for more details on how to include these keywords in the namelist. If the files are kept anywhere other than the default locations listed below, the keywords must include the full path to the file.

IMAGE_STACK_FILE_NAME = <datafilename>
where <datafilename> = text file containing the list of data frames. The default location for this file is in the current working directory.

SIGMALIST_FILE_NAME = <sigmafilename> (optional)
where <sigmafilename> = text file containing the list of corresponding uncertainty images. Default location is the current working directory

DCE_STATUS_MASK_LIST = <DCEmaskfilename> (optional)
where <DCEmaskfilename> = text file containing the list of corresponding mask imges, flagging temporarily bad pixels. Default location is the current working directory.

PMASK_FILE_NAME = <pmaskfilename> (optional)
where <pmaskfilename> = relevant PMask file, flagging permanently bad pixels in the array. The default location for the PMask file is in a subdirectory, cal/ of the current working directory.

FIF_FILE_NAME = <FIFfilename> (optional)
where <FIFfilename> = name of the FIF.tbl file. This file is usually generated by Overlap, by running the Fiducial Image Frame Module. This keyword gives the option to use a previously-generated FIF.tbl file as input (e.g. if you wish to put the IRAC Channel 3 data on the same FIF as the Channel 1 data, or to use the FIF.tbl generated by a previous run of overlap.pl). Default location is the output directory.

OUTPUT_DIR = <output directory> (optional)
The default output directory is the current working directory. The default directories for the indiviual module outputs can also be changed - see the pages for the individual modules for the default output directory and the namelist keyword required to change it.

B: Fatal Bit Patterns

See MOPEX Input Namelist and Appendix 2: Fatal Bit Patterns for more information.

DCE_Status_Mask_Fatal_BitPattern = <DCE Status Mask Fatal Bit Pattern>

PMask_Fatal_BitPattern = <PMask Fatal Bit Pattern>

C: Other Options

All other options that can be set in the Global Parameters section of the Overlap namelist are all listed below. In order to activate these options, they must be specified with a value of 1, e.g. adding a line into your overlap namelist that reads:

save_namelist = 1

will turn on the "save namelist" option. Note the spaces before and after the "=" sign. The default for all options is "0", i.e. "off", unless otherwise specified. The options are listed in alphabetical order, but can be given in any order in the namelist.


compute_uncertainties_internally

Default = "1". If you do not have (or do not trust) your set of uncertainty images, this option will instruct MOPEX to execute the S/N Estimator module in an attempt to internally estimate the uncertainty in the input pixels. This option is over-ridden by have_uncertainties. If neither compute_uncertainties_internally or have_uncertainties is set then MOPEX will run S/N Estimator by default.

delete_intermediate_files

Gives the option to delete all of the intermediate files created in this run, except for the files created by the final module. Useful for saving disk space once you are satisfied with your reduction setup.

have_uncertainties

MOPEX will use the input uncertainty images given in the input keyword SIGMALIST_FILE_NAME (see MOPEX Input for uncertainty image details). The input uncertainty images will be interpolated and co-added, and may optionally be used in the co-addition of the interpolated data images (see the sigma_weighted_coadd option). This option overrides the default compute_uncertainties_internally option.

MARGIN

Specifies a margin in terms of the number of pixels around the FIF. Normally this is set to zero or a (small) positive number, except when running Mosaic Geometry, when it should normally be set to a negative number to avoid including input images that have only marginal overlap with the FIF.

mask_bright

Gives the option to use the bright object masks created by the Medfilter and Detect (Outlier) modules when interpolating the input images onto the FIF. Bright objects can bias the background levels of the images in which they are present. If the final overlap-corrected mosaic still looks "patchy", try re-running Overlap using bright object masking.

mosaic_corrected_images

Runs the Quicklook Mosaic module to create a quick and dirty mosaic of the background-corrected input images so that the user can check the results of the Overlap pipeline. In order to use this option, the parameter block for Mosaic Coadd must be included in the namelist.

MOSAIC_PIXEL_RATIO_X,
MOSAIC_PIXEL_RATIO_Y

The ratio of the input pixel pixel x, y size to the output mosaic pixel x, y size. Default = "1". The ratio is taken after correction for geometric distortion. This is overridden by MOSAIC_PIXEL_SIZE_X(Y), if specified.

MOSAIC_PIXEL_SIZE_X,
MOSAIC_PIXEL_SIZE_Y

The size in degrees of the output mosaic pixels in the x- and y-directions. MOSAIC_PIXEL_SIZE_X must be negative according to convention, else an error message will be generated. Specifying these values takes precedence over MOSAIC_PIXEL_RATIO_X(Y). The default pixel sizes depend on the instrument. See the instrument-specific namelists linked from the bottom of the MOPEX page for the default values for each channel.

NICE

NICE runs MOPEX with the UNIX command "nice 19". If you are not familiar with nice, click here for the Wikipedia description.

save_namelist

The namelist used in the current run is always copied to the output directory. By default, the name of the namelist is not changed. By setting save_namelist = 1, the namelist copied to the output directory is given a unique name, which is created by appending the namelist filename to the time of execution. For example, if you ran mosaic.pl -n myname.nl at 12:32:53, then the namelist will be copied to the output directory as 12h32m53s_myname.nl. The default is 0, in which case the file is copied as myname.nl and will be overwritten in subsequent runs that use the same namelist.

USE_REFINED_POINTING

Use the alternate FITS pointing keywords created by the offline pointing refinement script (pointing_refine.pl). Do not switch this on unless you have manually run pointing refinement outside of the normal BCD pipeline products.

verbose

Instructs MOPEX to print the output from each individual module. This is extremely useful for troubleshooting. If MOPEX encounters a problem while verbose is turned off, it may stop without printing an error message.