MOPEX Online Manual

Input Namelist

The namelist file for each of the processing scripts contains all of the input parameters to be used by MOPEX. Namelists can either be set up in a text file for use on the command line, or set up within the GUI. Namelists can be imported into/exported from the GUI and are interchangeable between the two versions of MOPEX. While the underlying code for MOPEX is identical for both the GUI and the command line, some of the parameter names were changed in the GUI to make their function clearer. Links to lists of all of the parameter names in the GUI and on the command line can be found near the bottom of the main MOPEX page

The namelist must be saved in a subdirectory of the working directory called <working_dir>/cdf/. Specifying a full path name to the namelist when calling MOPEX will not over-ride this.

An example of a namelist can be found here.

The namelist has the following structure:

1. Processing flow control: depending on the options you wish to use when running MOPEX, you will want to run some of the available modules but not others. This first part of the namelist controls the switching on and off of modules in the processing flow by setting "triggers" (keywords) for the modules to 1 or 0. For example:
   
   run_medfilter = 1 indicates "run the MedFilter module"
   run_medfilter = 0 indicates "do not run the MedFilter module"
   run_mosaic_dual_outlier = 1 indicates "run the Mosaic Dual Outlier module" etc.
   


2. Global parameters: a list of input parameters that are common to all modules, e.g. input files, pixel sizes, etc. For example:
   
   IMAGE_STACK_FILE_NAME = /home/joe/data/IRAC/ch1/bcd/ImageList.txt
   MOSAIC_PIXEL_SIZE_X = -0.00033889
   MOSAIC_PIXEL_SIZE_Y = 0.00033889
   OUTPUT_DIR = /home/joe/data/IRAC/ch1/Mosaic


3. Module parameter blocks: for each module, a set of input parameters specific to that module must be given. For example:
   
   &MEDFILTER
    Window_X = 45,
    Window_Y = 45,
    N_Outliers_Per_Window = 500,
   &END

Module triggers, settings, names and parameters, both inside and outside the module blocks, can be given in any order. Their order in the namelist will not affect the order in which they are run by MOPEX.

IMPORTANT NOTE: all input variables in the namelists require a space preceeding and following the equals sign, i.e. "variable = value". An entry like "variable=value"will not be read and the hard-coded default will be used. You will not be warned that your input value is not being read.

Depending on the pipeline you are intending to run (e.g. Overlap, Mosaic, APEX), you will need to activate different modules in your namelist. For more information on which modules you are likely to need, you should see Which Modules Should I Choose? and the example instrument-specific namelists linked at the bottom of the MOPEX page. For example, if you are planning to run the Background Matching (Overlap) pipeline then you may choose to run the Fiducial Image Frame, Mosaic Interpolate and Compute Overlap Correction modules, and then apply the correction to your images. In this case you would include the following lines in your namelist:

run_fiducial_image_frame = 1
run_mosaic_int = 1
compute_overlap_correction = 1
apply_overlap_correction = 1

The keywords required to run each module are given on the individual module help pages (along with input/output requirements, the keyword needed to change theoutput directory, and an in-depth discussion of the purpose of the module) and in the table in Appendix 3: MOPEX Module List.

If a module is turned on in the pipeline then a corresponding parameter block must be included in the namelist. For more detailed information on each pipeline and each module, please follow the link to the relevant pipeline- or module-specific page from the Manual Contents page.

2. Global Parameters Outside the Module Blocks

There are 3 main types of information in the Global Parameters section: Input/Output file and directory names; Fatal Bit Patterns for use with the Spitzer mask files; and more general options that control preferences in how the processing is carried out. For a full list of global parameter keywords that can be set from within the namelist, please see the Namelist Options pages for Background Matching (Overlap), Mosaic and Point Source Extraction (APEX).

A: Input Files and Output Directories

The namelist can be used to specify the input files and output directories for each module, instead of specifying them on the command line when running a pipeline. The namelist also allows you to customise the output directory name for each processing script, and each module within that script. The default output directory for all the scripts is the current working directory. To change this you should add the following line into your namelist:

OUTPUT_DIR = <your choice of output dir>

All modules have a default output directory that is a subdirectory of OUTPUT_DIR. In order to change these you should add lines similar to the one above into your namelist. The specific keyword you need to change the output directory of each module is given on the individual module help pages, along with the default directory name. For example, in order to change the output directory for the MedFiler module, look up the MedFilter Module page, find the "Output Directory Keyword: MEDFILTER_DIR" at the top of the page, and set the new directory name by adding the keyword into your namelist:

MEDFILTER_DIR = <your new medfilter output dir>

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 links from the IRAC and MIPS Data Products pages, and Chapter 9 of the IRS Data Handbook (pdf). When running MOPEX, you need to decide which of these bits 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 Bit Pattern" 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 Bit Pattern to: (2⁷ + 2⁸ + 2⁹ + 2¹⁰ + 2¹⁴) = 18304, and 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 with the keywords DCE_Status_Mask_Fatal_BitPattern and RMask_Fatal_BitPattern. The most up-to-date recommended Fatal Bit Patterns for each instrument are listed in the relevant sample namelists linked at the bottom of the MOPEX page.

The global parameters that can be specified outside the module blocks vary from pipeline to pipeline. Options include e.g. creating different types of mosaics, choosing whether MOPEX should print error messages to the command line, or whether the intermediate steps in the processing should be saved or not. A full list of the options available for each pipeline can be found on the Namelist Options pages for the pipelines (Overlap, Mosaic and Point Source Extraction (APEX)).

3. Module Parameter Blocks