MOPEX Online Manual

Introducing the Major Scripts in MOPEX

The five major scripts available in MOPEX are as follows:

1. overlap.pl: Background Matching. Performs background matching of the input BCD images to bring them to a common background level
2. mosaic.pl: Mosaicking. Interpolates the input images onto a common grid, carries out outlier detection and masking, co-adds the images together and stitches them all into a single mosaic
3. apex.pl: APEX Multiframe. Carries out point source extraction by simultaneously fitting the point response function in all of the BCDs. This is recommended if there are enough detected sources in the BCDs to generate a good PRF and is useful for data with intra-pixel variability (e.g. IRAC data) or where the PRF varies across the array (e.g. MIPS). Point source detection and aperture photometry are carried out on the mosaicked image.
4. apex_1frame.pl: APEX Single Frame. Carries out point source extraction on the mosaic image, using a user-specified PRF image. An alternative to apex.pl if there are not enough detectable sources in the BCDs to fit the PRF.
5. apex_qa.pl: APEX QA. Creates residual images for both apex.pl and apex_1frame.pl by subtracting the detected point sources from the input images. This module is invaluable for checking the results of PRF-fitting. Available only on the command-line, not yet in the GUI.

Each of these scripts has a wealth of options associated with it that are set in the parameter file, or "namelist" for the script. The namelist specifies everything from input and output directory names to the processing options that should be used, and the output files that should be generated. More information on the structure and syntax of the namelist can be found on the MOPEX Input Namelist page.

Ancillary Scripts

While the five major scripts above are the most commonly used, there are many more that are available on the command-line. A full list of all of the MOPEX scripts can be found in Appendix 1: Full List of MOPEX Scripts, but the most commonly used ones are:

• flatfield.pl: Produces final flat-fielded BCDs for MIPS data that can be input into the Mosaic pipeline. Incorporates background subtraction, bright object masking and flatfielding, and allows the optional input of mask files. Intended to isolate artifacts such as jailbars and bright and dark latents and remove them from the affected BCDs. See README_flatfield (txt file) for documentation.
• mosaic_sed.pl: MIPS SED data reduction. This script performs interpolation and coaddition of MIPS SED (spectral energy distribution) images, and extracts the spectra. See mosaic_sed.pdf for documentation.
• prf_estimate.pl: PRF Estimation. Standard PRFs for point source fitting are provided with MOPEX, but in some cases users may wish to generate their own PRF from their dataset. This script takes a list of APEX-deteced sources and uses them to generate a new PRF. Warning: Only for use with well-sampled data that does not display any intra-pixel variability. For this reason, this script should not be used with IRAC data. See PRF_estimate.pdf for documentation.