MOPEX User's Guide - IRSA

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1.5 How To Use This Manual This manua l is split into the following parts: MOPEX User’s Guide • Introductory material for MOPEX in general, including installation instructions and a quick start guide; • An overview of the software and its capabilities; • Input files and requirements for MOPEX; • An in-depth description of all the pipelines and modules available in MOPEX; • Basic Concepts in MOPEX, with in-depth discussions of the algorithms implemented; • Running MOPEX on the command line; • Appendices, with useful tables and supplementary material. The bulk of this document describes how to run MOPEX from the GUI, but Chapter 9 provides details of how to run MOPEX from the command line. For the purposes of this manual, we will call the directory containing your data , the directory in which you have installed MOPEX , and the directory from which you are planning to run MOPEX (which may be the same as or but doesn’t have to be). 1.6 Installing MOPEX and Downloading Your Data MOPEX can be used to reduce all Spitzer data except for spectra from the IRS. This includes imaging with IRAC, MIPS and the IRS Peak-Up arrays, and MIPS SED mode. MOPEX is distributed as a package containing both the GUI and command-line versions, and is available at the following URL, with full download and setup instructions: http://irsa.ipac.caltech.edu/data/SPITZER/docs/dataanalysistools/tools/mopex/ If you are running MOPEX on a Mac, please ensure that you drag the MOPEX icon to either your Applications folder, or some other location with write privileges. MOPEX will not work if you try to run it from the read-only directory created by the .dmg file. Once you have installed MOPEX, start the GUI by double-clicking on the MOPEX icon, or by running the following on the command line: unix% //mopex Introduction 4 How To Use This Manual
for Linux and Solaris systems, and: unix% //mopex.app/Contents/MacOS/JavaApplicationStub on Macs. 1.6.1 Getting Spitzer Data MOPEX User’s Guide All Spitzer data are downloaded from the Spitzer Heritage Archive . You will be given a choice of data products to download. MOPEX is designed to use the Level 1 (Basic Calibrated Data; BCD) products as input, but the Level 2 (Post-BCD; PBCD) products are useful for quick looks. In general, the user should begin science reductions with the BCD products. Once you have downloaded your data, unpack the zip files into a data directory () of your choice. 1.7 Quickstart Guide To create a quick mosaic of Spitzer data using MOPEX, follow the steps below. This will only create a mosaic using a generic template, and may not be optimum for your data. 1. Start the GUI as described above; 2. Load a template namelist from the File menu by clicking on File > New Mosaic Pipeline; 3. Select from the drop-down menu, e.g. if you have IRAC channel 1 data, select Mosaic, IRAC ch1; 4. Create lists of your input files on the command line, e.g.: unix% ls //ch1/bcd/*bcd.fits > InputImageList.txt unix% ls //ch1/bcd/*bunc.fits > InputUncList.txt unix% ls //ch1/bcd/*bimsk.fits > InputMskList.txt (see Chapter 3 for more information on MOPEX input files); 5. Add the newly-created input list files into MOPEX. In the Initial Settings module: Image Stack File = InputImageList.txt Output Directory = /your/chosen/ And under Optional Input and Mask files: Introduction 5 Quickstart Guide
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OUTPUT None DISCUSSION MOPEX User
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MOPEX User’s Guide This module al
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MOPEX User’s Guide negative numbe
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DISCUSSION MOPEX User’s Guide For
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MOPEX User’s Guide then interpola
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MOPEX User’s Guide This module pe
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DISCUSSION MOPEX User’s Guide Mos
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PURPOSE MOPEX User’s Guide This m
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DISCUSSION No further information.
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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 is recorded as
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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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Condition Builder: Some simple sele
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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 USE_DUAL_OUTLI
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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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8.4.5 Cubic: Bicubic Interpolation
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z n = ∑ r(r≠n ) Onr(I n − Ir
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∑ AP = a i ⋅ I i MOPEX User’s
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8.9.3 Aperture Uncertainties MOPEX
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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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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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