MOPEX User's Guide - IRSA

Chapter 2. Overview of MOPEX
MOPEX User’s Guide
MOPEX was developed at the Spitzer Science Center to process Spitzer Level 1 Basic Calibrated
Data (BCD) from the point at which the users download the files from the archive through to final
point source extraction. While it is primarily designed to take Spitzer data as input, it is a generalpurpose
tool that can be applied to any images in standard FITS format (see §3.1 for MOPEX
input image requirements).
2.1 How MOPEX Works
The MOPEX software package is a set of Perl wrapper scripts that call C++ and C modules. For
the GUI, the Perl scripts were translated into Java. All of the Perl scripts can be found in the
MOPEX installation directory, under //bin/.
These scripts are incorporated into the GUI as pipeline flows, and each pipeline calls a series of
individua l modules in sequence. Depending on the options you wish to use when processing your
data, you will need to include different combinations of modules in a pipeline. For example, if
you want to use one of the outlier rejection algorithms to remove the cosmic rays from your final
mosaic, you need to set up the Mosaic flow to include the outlier rejection modules. Setups that
you choose for a pipeline can be saved as a parameter file called a “namelist”. This namelist can
be read back into the GUI at a later date. Default namelists are also provided.
2.2 How to run MOPEX in the GUI
When you first start the MOPEX GUI, you are presented with a blank screen. To begin using
MOPEX, you must initiate a pipeline from the File Menu. You can choose to initiate a pipeline in
three different ways - you can read in a previously-saved parameter file (called a “namelist”; File
> Read Namelist), you can start from a template of default modules and parameters (e.g. File >
New Mosaic Pipeline), or you can choose to begin with a blank pipeline and add modules one at a
time by hand (File > New Empty Mopex Pipeline). First time users are advised to begin with the
template pipelines. Each module has a help page that explains what it does, what the inputs mean,
and what outputs can be expected. The help page is accessed by the "?" button, or by reading the
module descriptions contained in this manual.
Usually you will start by loading a template namelist as your starting point. We will assume for
the moment that we have IRAC channel 1 data that we wish to background-match and mosaic
Overview of MOPEX 7
How MOPEX Works