MOPEX Online Manual

Background Matching (Overlap)

Purpose

The Overlap flow in MOPEX performs background matching between overlapping frames. An additive correction is calculated for each images in the input stack in order to bring them to a common background level. This pipeine is often the first step in processing Spitzer imaging data.

Overview

The Overlap pipeline begins with the stack of user-defined input images, specified either in the namelist or on the command line (see below for syntax). If uncertainty input files are not available (e.g. if you are not using Spitzer data), the uncertainties must be calculated using S/N Estimator. We strongly recommend using the uncertainty images that are provided with all Spitzer data. The output of the flow is a table of overlap correction factors and, usually, a stack of background-matched images. The output images do not have zero background; rather, a constant is added to each image in order to bring the background to a common level. These output images may be used as input to the later MOPEX flows. Additionally, a Quicklook Mosaic may be created using the already interpolated images.

Overlap finds the additive offsets for each frame so that the pixel differences in the overlap regions (after interpolation to a common grid) are minimized. The metric that is minimized is the sum of the uncertainty-weighted squared differences between overlapping pixels in all pairs of interpolated input images, however, this does not determine the overall level that the frames are corrected to. Two methods are implemented:

In the first method (WEIGHT=0, the default), MOPEX determines the overall level after finding the offsets, by forcing the sum of the offsets of all the images to add up to 0.

The offsets are analyzed before applying the above condition. The outliers are found using the namelist parameters BOTTOM_THRESHOLD and TOP_THRESHOLD in units of sigma, and MIN_IMG_NUM, the minimum number of images needed to detect outliers. This method should give good results for large numbers of frames without strong systematic deviations.

In the second method (nominally WEIGHT=1), Overlap minimizes the squared offsets as part of the original minimization. The user can experiment by sliding WEIGHT up or down, giving more or less weight to the squared offsets. In principle, this method should allow correction for offsets even for a small number of frames with a varying background, but the range of effectiveness has not been thoroughly tested.

The methods are described in the online document background_matching.pdf and the first is given in more detail in Makovoz et al. 2005, PASP 117, 274-280.

Optionally, the user can run an additional preprocessing step in order to detect and mask all bright objects in the input images that might adversely affect the process of background matching.

Overlap has a fault in that it finds additive corrections to all frames in one swoop. For a large number of frames, this leads to a big matrix inversion, requiring a big chunk of memory, so it can fail if the memory limit is reached. Common problems encountered with Overlap are:


1. Inclusion of wildly discrepant frames, e.g. MIPS70 or MIPS160 stim flashes, will give the algorithm trouble, and may cause Overlap to fail with the error message "UNSUCCESSFUL_SOLUTION". Make sure you have removed all of the stim flash frames before running MOPEX.
2. Systematic offsets with heavy overlap, e.g. at the start of MIPS24 scan legs, will not be corrected.

Running Overlap

Background matching is run on the command line using the script overlap.pl. The script expects a list of FITS images and a namelist file as input. The format of the input list is given on the Input Files page, and the format of the namelist is described at Input Namelist. The syntax for running Overlap is as follows:

prompt> overlap.pl <option flag> <specification>

where <option flag> and the associated <specification> are given below. The only option that must be specified on the command-line is the name of the namelist file. All other options (including the list of input images) can be set from within the namelist (recommended).




Option Flag	Specification File (example)	Default Location	Required/Optional
-n	namelist of input parameters (mosaic.nl)	./cdf/	required
-I	list of input images (ImageList.txt)	./	required
-S	list of input uncertainty images (SigmaList.txt)	./	optional
-d	list of DCE status mask images (IMaskList.txt)	./	optional
-M	permanently damaged pixel mask image (pmask.fits)	./cal/	optional
-F	Fiducial Image Frame file (FIF.tbl)	./<output directory>/	optional
-O	Output directory	./	optional