Supported Software: MOPEX

Purpose and Description

MOPEX (MOsaicker and Point source EXtractor) is the SSC's package for reducing and analyzing imaging data, as well as MIPS SED data. MOPEX includes the point source extraction package, APEX. The Spitzer data reduction pipeline produces individual Basic Calibrated Data (BCD) frames that can be input into MOPEX to produce mosaicked images before extracting the point sources with APEX or any other software of your choice.

MOPEX is designed to allow the user to:

• perform sophisticated background matching of individual data frames
• mosaic the individual frames downloaded from the Spitzer archive
• perform both temporal and spatial outlier rejection during mosaicking
• apply offline pointing refinement for MIPS data (refinement is already applied to IRAC data)
• perform source detection on the mosaics using APEX
• compute aperture photometry or PRF-fitting photometry for point sources
• perform interpolation, coaddition, and spectrum extraction of MIPS SED images.

The MOPEX GUI

The MOPEX GUI is designed to allow the user to interactively set the many parameters in the processing modules, and then to examine the output of each step. Template parameter sets are available as a starting point, but users are strongly recommended to evaluate the process as it applies to their own data. Different datasets require different choices. The GUI includes module-by-module online help to allow easy access to the documentation.

While the GUI provides an interactive interface to access the MOPEX software, the underlying scripts and binaries are the same as those available in the command-line interface. Scripts that run on the command line can be imported into the GUI, and settings selected in the GUI can be saved and exported for use on the command line. The scripts currently available through the GUI are overlap, mosaic, apex, apex_1frame, apex_qa and prf_estimate. Other useful scripts, such as flatfield are only available from the command line. Users are encouraged to check the full list of MOPEX scripts before writing their own code.

Supported Platforms: Solaris 10+, Mac OSX 10.3+, RedHat Linux, Windows.
The GUI may also run on other flavors of Linux. If you are successful in running the MOPEX GUI on any platform not listed above then please email us at the Spitzer Helpdesk so we can keep the User Community updated.

Command-Line MOPEX

The command-line version of MOPEX consists of a set of perl scripts that are called by the user from the command line. Some of these scripts aren't yet available in the GUI, but may be useful for data manipulation. Users are encouraged to check them before writing their own code. Experienced users, or those with large volumes of data may prefer to use the command-line version of MOPEX since it is marginally faster and can be scripted. Experienced users may still find the enhanced documentation included in the GUI useful.

The full list of scripts included with MOPEX can be found here.

Supported Platforms: Solaris 10+, Mac OSX 10.3+, RedHat Linux
The command-line version of MOPEX may also run on other flavors of Linux, and on Windows if you have "cygwin" installed. If you are successful in running command-line MOPEX on any platform not listed above then please email us at the Spitzer Helpdesk so we can keep the User Community updated.

Downloading and installing the software

Follow these instructions for downloading and installing the software.

Updating MOPEX

All updates are now done automatically through the GUI. To update either the GUI or the command-line version of MOPEX, start the GUI while connected to the internet. MOPEX will automatically download any available updates whenever it is restarted. To check for updates without re-starting MOPEX, go to the Options menu on the task bar and toggle Use Automatic Mopex Version Update off and back on again.

Getting Help

Support for MOPEX is available from the Spitzer Helpdesk but you can also check the extensive help function included in the GUI, the MOPEX Online Manual, the Data Reduction and Analysis Cookbooks, the list of common pitfalls listed below, the known bugs list and the FAQ page for answers to commonly asked questions.

Important Notes and Common Pitfalls

1. See the MOPEX Bug List for a list of known issues with the software. We are working to correct these for the next release.


2. New PRFs have been released for use with IRAC data, and can be found at http://ssc.spitzer.caltech.edu/irac/psf.html. More information on PRF fitting with IRAC data can be found at IRAC PRF Fitting.


3. We only support the command-line version of MOPEX running on Solaris 10+; RedHat Linux 8+; or Mac OSX 10.3+. It has come to our attention that many users running other flavours of Linux have experienced Perl library linking problems.We strongly recommend that users experiencing problems switch to the MOPEX GUI. For Debian users, the linking problems with the command-line version of MOPEX can sometimes be fixed by modifying the line below in the mopex.csh file (mopex-script-env.csh in the latest release).
   

   setenv LD_ASSUME_KERNEL 2.4.1 should be modified to read:

   setenv LD_ASSUME_KERNEL `uname -r`

4. In a MOPEX namelist, the input variables 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, so you will not notice that your input value is not being used.


5. Warning: namelists from versions of MOPEX released prior to March 2006 are not compatible with version mopex_030106 or later.

User's Guides

Online Manual for MOPEX

Overview of Post-BCD processing (pdf)

Pointing Refinement User's Guide (pdf)

Using APEX

Data Reduction and Analysis Cookbooks

List of known bugs in MOPEX

MOPEX FAQ

Previous Manuals (superseded by the online MOPEX manual)

Background Matching (overlap) User's Guide (pdf)

Mosaicker User's Guide (pdf)

APEX User's Guide (pdf)

Full list of documentation, including Data Analysis Cookbooks

Example namelists for MOPEX

The parameters set in these namelists are a reasonable starting point for most data sets, but not all. For example, BOTTOM_THRESHOLD and TOP_THRESHOLD parameters of outlier rejection (found under MOSAICOUTLIERIN) are presently set to 5 in the namelists for IRAC and MIPS-24, and to 3 for MIPS-70 and MIPS-160. However, these numbers are not optimal in all cases - a value of 5 is too low for IRAC coverage of ~50, and leads to false outlier detections (a value of 10 is more optimal). We recommend that users read the documentation linked at the top of this page, and experiment with the namelist settings to find the optimal settings for their dataset.

• Overlap Input Parameters
• Mosaic Input Parameters
• APEX (MultiFrame) Input Parameters
• APEX 1Frame Input Parameters
• APEX QA (MultiFrame) Input Parameters
• APEX QA 1Frame Input Parameters
• PRF Estimate Input Parameters