MOPEX User's Guide - IRSA

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MOPEX User’s Guide parameters before running your reduction. Alternatively, you can choose to build up your namelist from an empty pipeline by going to File > New Empty MOPEX Pipeline. Namelists can be written out to an ASCII file to save them for a later GUI reduction (File > Save As), or exported to command-line format to run them on the command line (File > Export Inner Pipeline), and namelists that have been set up on the command line (see Chapter 9) can be imported into the GUI and run there (File > Read Name List; this is valid for reading in both command-line and GUI namelists). The names of some of the parameters on the command line have been changed in the GUI to improve clarity. You can find a full list of all the input parameters for the GUI, along with the command-line counterparts, in the MOPEX glossary pages, linked from the MOPEX webpage. For more information on the structure of the saved ASCII file namelist and running MOPEX on the command line, see Chapter 9. MOPEX Input 22 MOPEX Input Namelist
Chapter 4. Overlap (overlap.pl) MOPEX User’s Guide The Overlap pipeline in MOPEX (on the command line, the script is overlap.pl) performs background matching between overlapping frames. An additive correction is calculated for each image in the input stack in order to bring them to a common background level. This is often the first step in processing Spitzer imaging data. 4.1 Overview To load an Overlap pipeline, either start from a MOPEX template namelist (File > New Overlap Pipeline), load an existing Overlap namelist file (File > Read Name List) or load an empty flow and insert an Overlap pipeline from there (File > New Empty MOPEX Pipeline, then go to Insert Overlap at the top of the flow window and choose Empty Pipeline). MOPEX will load an Overlap flow to which you can add and subtract modules, and modify the input parameters. For information on running Overlap on the command line, see Chapter 9. Overlap begins with a text list of input images (for Spitzer data, these are usually the Level 1 BCDs). This is loaded in Image Stack File, in the Initial Setup module. Uncertainty and mask files are loaded in Optional Input & Mask Files. The final output is a table of overlap correction factorsand a stack of offset-corrected images. If desired, a QuickLook mosaic can be created, incorporating the corrections. 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. If the user has no uncertainty files, Overlap can run a module called S/N Estimator, which estimates the uncertainties from the gain and read noise. The user should carefully read §4.3.3 to do this correctly. For Spitzer data, the pipeline uncertainties are generally preferred. 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. In the GUI, 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 (see §8.5 for a full description of the algorithm). The Overlap (overlap.pl) 23 Overview
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MOPEX User’s Guide processed in o
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MOPEX User’s Guide Min Pix Number
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MOPEX User’s Guide Box Median Bia
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MOPEX User’s Guide If coverage >=
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MOPEX User’s Guide Refine Outlier
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MOPEX User’s Guide Reinterpolatio
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PURPOSE MOPEX User’s Guide The in
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MOPEX User’s Guide The tile speci
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MOPEX User’s Guide Standard Devia
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Mosaic Coverage File (mosaic_cov.fi
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There are no user-defined input par
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COMMAND LINE INPUT See INPUT. OUTPU
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MOPEX User’s Guide limitations di
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6.3 Running APEX MOPEX User’s Gui
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MOPEX User’s Guide Point Source D
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Figure 6.1: Overview of the main pr
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Relevant Pipelines: All PURPOSE INP
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NICE = 1 save_namelist = 1 MOPEX Us
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MOPEX User’s Guide Mosaic PRF Fil
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create_unc_mosaic = 1 use_std_to_de
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MOPEX User’s Guide Use Refined Po
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MOPEX User’s Guide Here FLUXCONV
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MOPEX User’s Guide This module cr
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MOPEX User’s Guide year) and with
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MOPEX User’s Guide Mosaic FIF Tab
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MOPEX User’s Guide Tile BCD file
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MOPEX User’s Guide Window X, Y: (
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MOPEX User’s Guide neighboring pi
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⎛ ⎜ ⎜ P( j) = ⎜ 1+ ⎜ ⎜
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&END MOPEX User’s Guide if use_ps
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MOPEX User’s Guide \float Tile_Of
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MOPEX User’s Guide Input Type: De
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MOPEX User’s Guide This module co
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&END OUTPUT MOPEX User’s Guide Th
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INPUT Columns selection: MOPEX User
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PURPOSE MOPEX User’s Guide Fits t
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MOPEX User’s Guide given below. O
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6.5.19 APEX Modules: Aperture Photo
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MOPEX User’s Guide This module al
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Condition Builder: Some simple sele
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MOPEX User’s Guide Fatal Mask Bit
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MOPEX User’s Guide Pixel by Size:
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MOPEX User’s Guide Mosaic PRF Fil
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PRF_ResampleX_Factor = 100, PRF_Res
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7.3 Running PRF Estimate MOPEX User
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MOPEX User’s Guide 3. Outlier Rej
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PURPOSE MOPEX User’s Guide Set up
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MOPEX User’s Guide Most users wil
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DISCUSSION MOPEX User’s Guide Wit
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7.5.5 PRF Estimate Modules: Split B
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MOPEX User’s Guide Fit Seed: (int
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Chapter 8. Basic Concepts in MOPEX
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8.2 Outlier Detection MOPEX User’
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MOPEX User’s Guide Figure 8.3: An
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MOPEX User’s Guide Two ways to es
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MOPEX User’s Guide USE_DUAL_OUTLI
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MOPEX User’s Guide Figure 8.9: As
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MOPEX User’s Guide Important: Usi
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8.3.2 Thresholding MOPEX User’s G
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T cl = P min − T min SegLevel MOP
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Centroid _ X = ∑ i∈cluster X(i)
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MOPEX User’s Guide where IPi is t
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8.4.5 Cubic: Bicubic Interpolation
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z n = ∑ r(r≠n ) Onr(I n − Ir
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MOPEX User’s Guide the parameter
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MOPEX User’s Guide Figure 8.22: P
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MOPEX User’s Guide that resembles
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∑ AP = a i ⋅ I i MOPEX User’s
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MOPEX User’s Guide In particular
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8.9.3 Aperture Uncertainties MOPEX
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MOPEX User’s Guide e.g. if you wi
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MOPEX User’s Guide In order to ru
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MOPEX User’s Guide from the GUI,
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9.4.2.1 Input Files and Output Dire
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MOPEX User’s Guide Table 9.1: Lis
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9.7.2 APEX User List Multiframe (ap
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9.7.4 Single-frame mode (apex_1fram
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MOPEX User’s Guide Table 9.6: Lis
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Appendix A. Full List of MOPEX Scri
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A.1.3 Under Construction Running MO
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Appendix B. Full List of Modules in
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Mosaic Interpolate run_mosaic_int P
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Running MOPEX on the Command Line a
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B.5 PRF Estimate Modules Running MO
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Instrument PRF Samp c Norm Radius (
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Some Tips for MOPEX with Spitzer Da
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