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CUBISM User Manual

by J.D. Smith, Lee Armus, Brent Buckalew, Danny Dale, George Helou, Helene Roussel & Kartik Sheth

Edition 1.6, for CUBISM version 1.6, November, 2008

CUBISM, the CUbe Builder for IRS Spectral Mapping, is a package written in the Interactive Data Language (IDL), which supports the analysis and reduction of spectral maps created with the IRS Spectrograph aboard the Spitzer Space Telescope.

1. Introduction  
2. Installation  
3. Quick Start Guide  
4. The Tools  
5. Cube Assembly  
6. Cube Analysis  
7. Tips and Troubleshooting  
Index   
 --- The Detailed Node Listing ---

Installation
2.1 Source Installation  
2.2 Binary Installation  
2.3 Setup  
2.4 Memory Requirements  
2.5 Running  
2.6 Upgrading   
Running
2.5.1 Running the Source Distribution  
2.5.2 Running the Binary Distribution   
Quick Start Guide
3.1 Example Data Set  
3.2 Building Your First Cube  
3.3 Visualizing the AORs  
3.4 Navigating the Cube   
The Tools
4.1 Tool Inter-Communication  
4.2 General Interface Tips  
4.3 CUBISM Project  
4.4 CubeView  
4.5 CubeSpec  
4.6 CubeSpec Plot Window   
General Interface Tips
4.2.1 List Selection  
4.2.2 Scrolling  
4.2.3 Mouse shortcuts  
4.2.4 File Selection   
CUBISM Project
4.3.1 Project Title  
4.3.2 Menus  
4.3.3 Data Records  
4.3.4 Status Bar  
4.3.5 Button Bar   
Menus
4.3.2.1 File Menu  
4.3.2.2 Edit Menu  
4.3.2.3 Record Menu  
4.3.2.4 Cube Menu  
4.3.2.5 Background Menu  
4.3.2.6 BadPix Menu  
4.3.2.7 Info Menu  
4.3.2.8 Help Menu   
Data Records
4.3.3.1 Record Info  
4.3.3.2 Record Enabled State  
4.3.3.3 Record Data Types  
4.3.3.4 Operating on Records   
CubeView
4.4.1 Title Bar  
4.4.2 Menus  
4.4.3 CubeView Tools  
4.4.4 Colorbar  
4.4.5 Status Display Line  
4.4.6 Bad Pixel Codes  
4.4.7 Image Info Block  
4.4.8 WAVSAMP Pane   
Menus
4.4.2.1 File Menu  
4.4.2.2 Options Menu  
4.4.2.3 Tools Menu   
CubeView Tools
4.4.3.1 Tool Interaction  
4.4.3.2 Box Regions  
4.4.3.3 Tool Overview  
4.4.3.4 Zoom Tool  
4.4.3.5 Histogram Tool  
4.4.3.6 Color Tool  
4.4.3.7 Image Slicing Tool  
4.4.3.8 Box Statistics Tool  
4.4.3.9 Aperture Photometry Tool  
4.4.3.10 Cube Extraction Tool  
4.4.3.11 Pixel Backtracking Tool  
4.4.3.12 Bad Pixel Tool  
4.4.3.13 AOR Visualization Tool  
4.4.3.14 Pixel Table Tool  
4.4.3.15 Order Mask Tool  
4.4.3.16 Compass Rose Tool   
CubeSpec
4.5.1 Title Bar  
4.5.2 Menus  
4.5.3 Buttons  
4.5.4 Display Panes   
Menus
4.5.2.1 File Menu  
4.5.2.2 Maps Menu   
Cube Assembly
5.1 Input Files  
5.2 Build Order  
5.3 Calibration Sets  
5.4 Backgrounds  
5.5 Bad Pixels  
5.6 Cube Build Settings  
5.7 WAVSAMP  
5.8 Building the Cube  
5.9 QuickBuild  
5.10 Saving the Project  
5.11 Saving the Cube as FITS  
5.12 Reading a FITS Cube   
Backgrounds
5.4.1 In Situ Background  
5.4.2 Archive Background  
5.4.3 Background Blend  
5.4.4 1D Sky Spectrum  
5.4.5 Combined 1D and 2D Background  
5.4.6 No Background  
5.4.7 Background Selection Using Visualization  
5.4.8 Saving the Background List   
Bad Pixels
5.5.1 Global and Record Level Bad Pixels  
5.5.2 Manual Bad Pixel Selection  
5.5.3 Backtracking to Discover Bad Pixels  
5.5.4 Automatic Bad Pixels  
5.5.5 Saving Bad Pixels   
Cube Analysis
6.1 Extracting 1D Spectra  
6.2 Creating 2D Maps  
6.3 Complex Maps   
Extracting 1D Spectra
6.1.1 Direct Extraction  
6.1.2 Matched Region Extraction   
Creating 2D Maps
6.2.1 User-defined Maps  
6.2.2 Pre-defined Maps  
6.2.3 Map Sets  
6.2.4 Redshift and Maps  
6.2.5 Integrated Maps  
6.2.6 Wavelength Weighting  
6.2.7 Line Fits   
Tips and Troubleshooting
7.1 Mouse and Keyboard Shortcuts  
7.2 Tips  
7.3 Troubleshooting  
7.4 Debugging CUBISM   
Mouse and Keyboard Shortcuts
7.1.1 Cube Project  
7.1.2 Cube View  
7.1.3 Cube Spec   










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