Spitzer Documentation & Tools
MOPEX User's Guide



Chapter 1.          Introduction.

1.1        Important Documentation.

1.2        User Interface.

1.3        Getting Help.

1.4        Why MOPEX?.

1.5        How To Use This Manual

1.6        Installing MOPEX and Downloading Your Data.

1.6.1         Getting Spitzer Data.

1.7        Quickstart Guide.

Chapter 2.          Overview of MOPEX

2.1        How MOPEX Works.

2.2        How to run MOPEX in the GUI

2.2.1         Encountering Error Messages in MOPEX.

2.3        Basic Processing Steps in MOPEX

2.3.1         Additional Functionality.

2.3.2         Expected Input

2.4        Introducing the Major Pipelines in MOPEX

2.4.1         Ancillary Scripts.

2.5        Which Modules Should I Choose?.

2.5.1         Overlap (overlap.pl)

2.5.2         Mosaic (mosaic.pl)

2.5.3         APEX Single Frame (apex_1frame.pl)

2.5.4         APEX Multiframe (apex.pl)

2.5.5         APEX User List (apex_user_list.pl; apex_user_list_1frame.pl)

2.5.6         APEX QA: Residual Image Creation (apex_qa.pl)

2.5.7         PRF Estimate (prf_estimate.pl)

Chapter 3.          MOPEX Input

3.1        MOPEX Input Images.

3.1.1         Spitzer Image Files.

3.1.2         Additional Mask Files.

3.2        MOPEX Input List Files.

3.3        MOPEX Input Namelist

Chapter 4.          Overlap (overlap.pl)

4.1        Overview

4.2        Overlap Processing Stages.

4.3        Overlap Modules.

4.3.1         Overlap Modules: Initial Setup.

4.3.2         Overlap Modules: Overlap Settings.

4.3.3         Overlap Modules: S/N Estimator.

4.3.4         Overlap Modules: Fiducial Image Frame.

4.3.5         Overlap Modules: MedFilter.

4.3.6         Overlap Modules: Detect

4.3.7         Overlap Modules: Mosaic Interpolate.

4.3.8         Overlap Modules: Compute Overlap Correction.

4.3.9         Overlap Modules: Quicklook Mosaic.

Chapter 5.          Mosaicking  (mosaic.pl)

5.1        Basic Input Requirements.

5.2        Running Mosaic.

5.3        Mosaicking a Portion of the Total FIF.

5.4        Creating a Mosaic of a Moving Object

5.5        Mosaic Pipeline Stages.

5.6        Mosaic Modules.

5.6.1         Mosaic Modules: Initial Setup.

5.6.2         Mosaic Modules: Mosaic Settings.

5.6.3         Mosaic Modules: S/N Estimator.

5.6.4         Mosaic Modules: Fiducial Image Frame.

5.6.5         Mosaic Modules: Mosaic Geometry.

5.6.6         Mosaic Modules: MedFilter.

5.6.7         Mosaic Modules: Detect Radhit

5.6.8         Mosaic Modules: Mosaic Interpolate.

5.6.9         Mosaic Modules: Detect

5.6.10      Mosaic Modules: Mosaic Projection.

5.6.11      Mosaic Modules: Mosaic Coverage.

5.6.12      Mosaic Modules: Mosaic Dual Outlier.

5.6.13      Mosaic Modules: Level

5.6.14      Mosaic Modules: Mosaic Outlier.

5.6.15      Mosaic Modules: Mosaic Box Outlier.

5.6.16      Mosaic Modules: Mosaic RMask.

5.6.17      Mosaic Modules: Mosaic Reinterpolate.

5.6.18      Mosaic Modules: Fix Coverage.

5.6.19      Mosaic Modules: Mosaic CoAdder.

5.6.20      Mosaic Modules: Mosaic Combine.

5.6.21      Mosaic Modules: Mosaic MedFilter.

5.6.22      Mosaic Modules: Create RMask Mosaic.

5.6.23      Mosaic Modules: Make Array Correction Files.

5.6.24      Mosaic Modules: Make Array Correction Mosaic.

Chapter 6.          Point Source Extraction (APEX)

6.1        Overview

6.1.1         APEX Multiframe (apex.pl)

6.1.2         APEX Single Frame (apex_1frame.pl)

6.1.3         APEX User List Multiframe (apex_user_list.pl)

6.1.4         APEX User List Single Frame (apex_user_list_1_frame.pl)

6.1.5         Aperture Photometry on Fixed Positions.

6.1.6         Residual Image Creation (apex_qa.pl)

6.2        Basic Input Requirements.

6.3        Running APEX

6.3.1         Using a Previously-Generated Mosaic with APEX.

6.4        APEX Processing Stages.

6.5        APEX Modules.

6.5.1         APEX Modules: Initial Setup.

6.5.2         APEX Modules: APEX Multiframe and APEX User List Multiframe Settings.

6.5.3         APEX Modules: APEX Single Frame and APEX User List Single Settings.

6.5.4         APEX Modules: S/N Estimator.

6.5.5         APEX Modules: Fiducial Image Frame.

6.5.6         APEX Modules: Mosaic Interpolate.

6.5.7         APEX Modules: Mosaic CoAdder.

6.5.8         APEX Modules: Detect MedFilter.

6.5.9         APEX Modules: Point Source Probability.

6.5.10      APEX Modules: Gaussnoise.

6.5.11      APEX Modules: Bright Detect

6.5.12      APEX Modules: Detect

6.5.13      APEX Modules: Mosaic Combine.

6.5.14      APEX Modules: Extract MedFilter.

6.5.15      APEX Modules: Fit Radius.

6.5.16      APEX Modules: Select Detect

6.5.17      APEX Modules: Detection Map.

6.5.18      APEX Modules: Source Estimate.

6.5.19      APEX Modules: Aperture Photometry.

6.5.20      APEX Modules: Select

6.6        APEX QA Modules.

6.6.1         APEX QA Modules: Initial Setup.

6.6.2         APEX QA Modules: APEX QA Settings (Multiframe)

6.6.3         APEX QA Modules: APEX QA Settings (Single Frame)

6.6.4         APEX QA Modules: (Mosaic) Point Source Image.

Chapter 7.          PRF Estimate.

7.1        Overview

7.2        Basic Input Requirements.

7.3        Running PRF Estimate.

7.4        PRF Estimate Processing Stages.

7.5        PRF Estimate Modules.

7.5.1         PRF Estimate Modules: Initial Setup.

7.5.2         PRF Estimate Modules: PRF Estimate Initial Setup.

7.5.3         PRF Estimate Modules: MedFilter.

7.5.4         PRF Estimate Modules: Crop Stack.

7.5.5         PRF Estimate Modules: Split By Array Position.

7.5.6         PRF Estimate Modules: PRF Estimate.

Chapter 8.          Basic Concepts in MOPEX

8.1        Tiling.

8.2        Outlier Detection.

8.2.1         Single Frame Outlier Rejection.

8.2.2         MultiFrame Temporal Outlier Detection.

8.2.3         Dual Outlier Detection.

8.2.4         Box Outlier Detection.

8.3        Image Segmentation.

8.3.1         Overview

8.3.2         Thresholding.

8.3.3         Co-added Images.

8.3.4         Probability Images.

8.3.5         Passive Deblending.

8.3.6         Centroid.

8.4        Image Interpolation.

8.4.1         Overview

8.4.2         Default: Pixel Overlap Integration.

8.4.3         Drizzle: Pixel Overlap Distribution.

8.4.4         Grid Distribution.

8.4.5         Cubic: Bicubic Interpolation.

8.5        Background Matching Algorithm

8.6        PRF fitting in MOPEX

8.6.1         Simplex Algorithm Modification.

8.7        Point Response Function.

Variable PRF.

8.8        Aperture Photometry.

8.9        Uncertainty Estimation.

8.9.1         delta_flux.

8.9.2         SNR Computation.

8.9.3         Aperture Uncertainties.

8.10      The User List Input Table.

8.11      Fatal Mask Bit Patterns.

Chapter 9.          Running MOPEX on the Command Line.

9.1        Setting up MOPEX

9.2        Setting up the MOPEX directory structure.

9.3        Running MOPEX

9.4        MOPEX Input Namelist

9.4.1         Processing Flow Control

9.4.2         Global Parameters Outside the Module Blocks.

9.4.3         Module Parameter Blocks.

9.5        Running Overlap on the command line.

9.6        Running Mosaic on the command line.

9.7        Running APEX on the command line.

9.7.1         APEX Multiframe (apex.pl)

9.7.2         APEX User List Multiframe (apex_user_list.pl)

9.7.3         APEX QA Multiframe (apex_qa.pl)

9.7.4         Single-frame mode (apex_1frame.pl)

9.7.5         APEX User List Single Frame (apex_user_list_1frame.pl)

9.7.6         Single Frame Residual Image Creation (apex_qa.pl)

9.8        Running PRF Estimate on the command line.

Appendix A.     Full List of MOPEX Scripts.

A.1       Supported Scripts.

A.1.1        Commonly Used.

A.1.2        Auxiliary.

A.1.3        Under Construction.

Appendix B.      Full List of Modules in MOPEX

B.1        Overlap Modules.

B.2        Mosaic Modules.

B.3        APEX (User List) and APEX (User List) 1Frame Modules.

B.4        APEX QA Modules.

B.5        PRF Estimate Modules.

Appendix C.     PRF Fitting Correction Factors for APEX:   Version 1 (10/20/2010)

Appendix D.     Some Tips for MOPEX with Spitzer Data:   Version 1 (3/16/2012)

D.1  Mosaics (IRAC and MIPS)

D.2  Fluxes and Uncertainties (IRAC and MIPS)

D.3 Point-Source Fitting: Apex for IRAC stacks, Apex_1frame for MIPS mosaic.

D.4  Use the Mosaic Task to make Mosaics (IRAC data)