MOPEX Online Manual
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Mosaic Namelist Options
For the format of the namelist, see MOPEX Input Namelist. This page gives a full list of the options available in the Global Parameters section of the Mosaic namelist. If you specify any mask files as input, you must also specify a corresponding Fatal Bit Pattern. See MOPEX Input Namelist for more information.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 Mosaic. 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. MOPEX assumes that the PMask file. Default location is a subdirectory, cal/ of the current working directory.
RMASK_LIST = <rmaskfilename> (optional)
where <rmaskfilename> = text file containing a list of the corresponding mask images flagging pixels rejected as outliers. Default location is the current working directory.
FIF_FILE_NAME = <FIFfilename> (optional)
where <FIFfilename> = name of the FIF.tbl file. Default location is the output directory. 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>
The default output directory is the current working directory.
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>
RMask_Fatal_BitPattern = <RMask Fatal Bit Pattern>
C: Other Options
All other options that can be set in the Global Parameters section of the Mosaic 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 mosaic 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. The use of this option is not recommended for Spitzer data
create_box_outlier_mosaic
- Creates the mosaic of the box outlier maps. It is created by coadding the box outlier maps for each input image. The prerequisite for this is the module Mosaic Box Outlier.
create_dual_outlier_mosaic
- Creates the mosaic of the dual outlier maps. It is created by coadding the dual outlier maps for each input image. The prerequisite for this is the module Level, which produces the final dual outlier maps.
create_outlier_mosaic
- Creates a mosaic of the outlier maps. It is created by coadding the outlier maps produced for each input image. The prerequisite for this is the module Mosaic Outlier, which produces the outlier maps.
create_rmask_mosaic
- The RMask images are interpolated and co-added into a single mosaic (mosaic_rmask.fits). However, they are treated as regular images, so all the bit information is lost in the process.
create_std_mosaic
- Creates a mosaic giving an estimate of the standard deviation for each pixel in the output image. This mosaic is called mosaic_std.fits.
create_unc_mosaic
- Creates a mosaic of the coadded uncertainty images. The output mosaic is called mosaic_unc.fits.
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.
keep_coadded_tiles
- Keeps the individual coadded tiles that are combined into the mosaic. These tiles can be used as input into APEX, if you wish to use outlier rejection with the apex.pl script. In order to set them as input to APEX, you will need to set the APEX output directory to match the Mosaic output directory, and turn off the mosaicking option in apex.pl. APEX will then automatically use the co-added tiles as input.
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. See the Mosaic Introduction page for more information on mosaicking portions of the total available area.
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.
MOVING_OBJECT_MOSAIC (int)
- Create the mosaic in the rest frame of a moving object. The "stationary" frame is chosen with the value of this keyword, and all other images are shifted relative to the stationary frame. i.e. if MOVING_OBJECT_MOSAIC = 5, MOPEX uses the 5th frame in the input stack as the base image, and shifts all other images to put the moving object at the same sky position. This functionality is limited to Spitzer data. See the Mosaic Introduction page for more information on creating Moving Object Mosaics.
NICE
- NICE runs MOPEX with the UNIX command "nice 19". If you are not familiar with nice, click here for the Wikipedia description.
overwrite_dmask
- Tells MOPEX to update the DMask files when single frame outlier rejection is performed with the module Detect Radhit. MOPEX will overwrite the input files specified by DCE_STATUS_MASK_LIST (usually the IMask files for IRAC), resetting bit 9 according to the resuls of the Detect Radhit outlier rejection. The Detect Radhit module is not normally needed for Spitzer data, as Radhit outlier rejection is run by the SSC when creating the BCD files.
run_absolute_minimum_mosaic
- Warning: This is an input option into the Mosaic Coadder module. It creates an absolute minimum mosaic (mosaic.fits) and the corresponding uncertainty mosaic (mosaic_unc.fits). The mosaic pixel value is set to the input pixel value with the smallest absolute value in the stack of the interpolated images. The corresponding mosaic uncertainty pixel is set to the pixel value in the interpolated uncertainty image corresponding to the imterpolated image with the smallest absolute pixel value. Useful for outlier rejection.
run_median_mosaic
- Warning: This is an input option into the Mosaic Coadder module. It creates the mosaic by co-adding the input images and taking the median value of the pixel stack. Flux is not conserved. This option is useful for making a quick-look mosaic, but should never be used for science. Output mosaic is called mosaic.fits. The associated uncertainty mosaic (mosaic_unc.fits) is also created.
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.
sigma_weighted_coadd
- Warning: This is an input option into the Mosaic Coadder module. It gives the option to co-add the interpolated images by weighting them with the uncertainty images. NOT RECOMMENDED.
USE_BOX_OUTLIER_FOR_RMASK
- Uses the results of the Box Outlier Detection to create the RMask. The prerequisite for this option is the module Mosaic Box Outlier, which runs the Box Outlier Detection. Default is "0", in which case the results of Single Frame Outlier Detection are used instead.
USE_DUAL_OUTLIER_FOR_RMASK
- Uses the results of the Dual Outlier Detection to create the RMask. The prerequisite for this option is the module Mosaic Dual Outlier, which runs the Dual Outlier Detection. Default is "0", in which case the results of Single Frame Outlier Detection are used instead.
use_fixed_coverage
- Tells MOPEX to use the results from the module Fix Coverage to perform the image coaddition. If this switch is not turned on, MOPEX will not use the Fix Coverage output, even if the module is included in the namelist.
USE_FLIPPED_PMASK
- We strongly recommend using the PMask files provided with the MOPEX distribution, or downloadable from the SSC website. If you are using these recommended PMasks, this switch should be ignored. The Spitzer pipeline used to create the BCD files "flips" the data files for IRAC channels 1 & 2. The PMasks provided with your data download are not flipped, and so this switch tells MOPEX to flip them to match the orientation of the data frames. The PMasks provided with MOPEX and downloadable from the SSC website are already flipped, and can be applied directly to your BCDs.
USE_OUTLIER_FOR_RMASK
- Uses the results of the Multiframe Temporal Outlier Detection to create the RMask. The prerequisite for this option is the module Mosaic Outlier, which runs the Multiframe Temporal Outlier Detection. Default is "0", in which case the results of Single Frame Outlier Detection are used instead.
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.
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