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CASA User Reference & Cookbook Release 3.3.0


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Version: November 14, 2011

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CASA Synthesis & Single Dish Reduction
Reference Manual & Cookbook

Editor: Jürgen Ott – Project Scientist

Jeff Kern – CASA Project Manager

http://casa.nrao.edu

CASA Synthesis & Single Dish Reduction
Reference Manual & Cookbook, Version November 14, 2011, ©2011 National Radio Astronomy Observatory The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.

 

Contents
List of Tables
List of Figures
1 Introduction
 1.1 About This Release
 1.2 Obtaining CASA
  1.2.1 What’s New in Release 3.3.0
 1.3 CASA Basics — Information for First-Time Users
  1.3.1 Before Starting CASA
   1.3.1.1 Environment Variables
   1.3.1.2 Where is CASA?
  1.3.2 Starting CASA
  1.3.3 Ending CASA
  1.3.4 What happens if something goes wrong?
  1.3.5 Aborting CASA execution
  1.3.6 What happens if CASA crashes?
  1.3.7 Python Basics for CASA
   1.3.7.1 Variables
   1.3.7.2 Lists and Ranges
   1.3.7.3 Indexes
   1.3.7.4 Indentation
   1.3.7.5 System shell access
   1.3.7.6 Executing Python scripts
  1.3.8 Getting Help in CASA
   1.3.8.1 TAB key
   1.3.8.2 help <taskname>
   1.3.8.3 help and PAGER
   1.3.8.4 help par.<parameter>
   1.3.8.5 Python help
 1.4 Tasks and Tools in CASA
  1.4.1 What Tasks are Available?
  1.4.2 Running Tasks and Tools
   1.4.2.1 Aborting Synchronous Tasks
  1.4.3 Getting Return Values
  1.4.4 Running Tasks Asynchronously
   1.4.4.1 Monitoring Asynchronous Tasks
   1.4.4.2 Aborting Asynchronous Tasks
  1.4.5 Setting Parameters and Invoking Tasks
   1.4.5.1 The scope of parameters in CASA
   1.4.5.2 The default Command
   1.4.5.3 The go Command
   1.4.5.4 The inp Command
   1.4.5.5 The saveinputs Command
   1.4.5.6 The tget Command
   1.4.5.7 The tput Command
   1.4.5.8 The .last file
  1.4.6 Tools in CASA
 1.5 Getting the most out of CASA
  1.5.1 Your command line history
  1.5.2 Logging your session
   1.5.2.1 Startup options for the logger
   1.5.2.2 Setting priority levels in the logger
  1.5.3 Where are my data in CASA?
   1.5.3.1 How do I get rid of my data in CASA?
  1.5.4 What’s in my data?
  1.5.5 Data Selection in CASA
 1.6 From Loading Data to Images
  1.6.1 Loading Data into CASA
   1.6.1.1 VLA: Filling data from VLA archive format
   1.6.1.2 Filling data from UVFITS format
   1.6.1.3 Loading FITS images
   1.6.1.4 Concatenation of multiple MS
  1.6.2 Data Examination, Editing, and Flagging
   1.6.2.1 Interactive X-Y Plotting and Flagging
   1.6.2.2 Flag the Data Non-interactively
   1.6.2.3 Viewing and Flagging the MS
  1.6.3 Calibration
   1.6.3.1 Prior Calibration
   1.6.3.2 Bandpass Calibration
   1.6.3.3 Gain Calibration
   1.6.3.4 Polarization Calibration
   1.6.3.5 Examining Calibration Solutions
   1.6.3.6 Bootstrapping Flux Calibration
   1.6.3.7 Correcting the Data
   1.6.3.8 Splitting the Data
   1.6.3.9 UV Continuum subtraction
   1.6.3.10 Transforming the Data to a new frame
  1.6.4 Synthesis Imaging
   1.6.4.1 Cleaning a single-field image or a mosaic
   1.6.4.2 Feathering in a Single-Dish image
  1.6.5 Self Calibration
  1.6.6 Data and Image Analysis
   1.6.6.1 What’s in an image?
   1.6.6.2 Image statistics
   1.6.6.3 Image values
   1.6.6.4 Moments of an image cube
   1.6.6.5 Image math
   1.6.6.6 Regridding an Image
   1.6.6.7 Displaying Images
  1.6.7 Getting data and images out of CASA
2 Visibility Data Import, Export, and Selection
 2.1 CASA Measurement Sets
  2.1.1 Under the Hood: Structure of the Measurement Set
 2.2 Data Import and Export
  2.2.1 ALMA: Filling of Science Data Model (ASDM) data
   2.2.1.1 Filling SDM v0 data using importoldasdm
  2.2.2 EVLA: Filling of Science Data Model (ASDM) data
  2.2.3 VLA: Filling data from archive format (importvla)
   2.2.3.1 Parameter applytsys
   2.2.3.2 Parameter bandname
   2.2.3.3 Parameter frequencytol
   2.2.3.4 Parameter project
   2.2.3.5 Parameters starttime and stoptime
   2.2.3.6 Parameter autocorr
   2.2.3.7 Parameter antnamescheme
   2.2.3.8 Parameter evlabands
  2.2.4 UVFITS Import and Export
   2.2.4.1 Import using importuvfits
   2.2.4.2 Import using importfitsidi
   2.2.4.3 Export using exportuvfits
  2.2.5 Handling Measurement Set metadata and data
  2.2.6 Summarizing your MS (listobs)
  2.2.7 Listing MS data (listvis)
  2.2.8 Listing and manipulating MS metadata (vishead)
  2.2.9 MS statistics (visstat)
  2.2.10 Concatenating multiple datasets (concat)
 2.3 Data Selection
  2.3.1 General selection syntax
   2.3.1.1 String Matching
  2.3.2 The field Parameter
  2.3.3 The spw Parameter
   2.3.3.1 Channel selection in the spw parameter
  2.3.4 The selectdata Parameters
   2.3.4.1 The antenna Parameter
   2.3.4.2 The scan Parameter
   2.3.4.3 The timerange Parameter
   2.3.4.4 The uvrange Parameter
   2.3.4.5 The msselect Parameter
3 Data Examination and Editing
 3.1 Plotting and Flagging Visibility Data in CASA
 3.2 Managing flag versions with flagmanager
 3.3 Flagging auto-correlations with flagautocorr
 3.4 X-Y Plotting and Editing of the Data
  3.4.1 MS Plotting and Editing using plotms
   3.4.1.1 Loading and Selecting Data
   3.4.1.2 A Brief Note Regarding plotms Memory Usage
   3.4.1.3 Plot Axes
   3.4.1.4 Tools
   3.4.1.5 Interactive Flagging in plotms
   3.4.1.6 Averaging Data
   3.4.1.7 Plot Symbols
   3.4.1.8 Summarizing Data
   3.4.1.9 Defining Frequency and Velocity
   3.4.1.10 Shifting the Phase Center
   3.4.1.11 Plot Ranges
   3.4.1.12 Plot Labels
   3.4.1.13 Grid Lines
   3.4.1.14 Legend
   3.4.1.15 The Options Tab
   3.4.1.16 Iteration
   3.4.1.17 Saving your plot
   3.4.1.18 Exiting plotms
  3.4.2 Plotting and Editing using plotxy
   3.4.2.1 GUI Plot Control
   3.4.2.2 The selectplot Parameters
   3.4.2.3 The iteration parameter
   3.4.2.4 The overplot parameter
   3.4.2.5 The plotrange parameter
   3.4.2.6 The plotsymbol parameter
   3.4.2.7 The showflags parameter
   3.4.2.8 The subplot parameter
   3.4.2.9 Averaging in plotxy
   3.4.2.10 Interactive Flagging in plotxy
   3.4.2.11 Flag extension in plotxy
   3.4.2.12 Setting rest frequencies in plotxy
   3.4.2.13 Printing from plotxy
   3.4.2.14 Exiting plotxy
   3.4.2.15 Example session using plotxy
  3.4.3 Plotting antenna positions using plotants
 3.5 Non-Interactive Flagging using flagdata2
  3.5.1 Flag Antenna/Channels
   3.5.1.1 Manual flagging and clipping in flagdata
   3.5.1.2 Flagging the beginning of scans
   3.5.1.3 Flagging shadowed data with mode ’shadow’
   3.5.1.4 Autoflagging.
 3.6 Command-based flagging using flagcmd
  3.6.1 Input modes flagmode
   3.6.1.1 Input flag mode ’table’
   3.6.1.2 Input flag mode ’xml’
   3.6.1.3 Input flag mode ’file’
   3.6.1.4 Input flag mode ’cmd’
  3.6.2 Operation types optype
   3.6.2.1 Apply flags — optype option ’apply’
   3.6.2.2 Unapply flags — optype option ’unapply’
   3.6.2.3 Save flags — optype option ’save’
   3.6.2.4 List flags — optype option ’list’
   3.6.2.5 Plot flags — optype option ’plot’
   3.6.2.6 Clear flags — optype option ’clear’
   3.6.2.7 Set flags — optype option ’set’
  3.6.3 Flagging command syntax
 3.7 Browse the Data
4 Synthesis Calibration
 4.1 Calibration Tasks
 4.2 The Calibration Process — Outline and Philosophy
  4.2.1 The Philosophy of Calibration in CASA
  4.2.2 Keeping Track of Calibration Tables
  4.2.3 The Calibration of VLA data in CASA
  4.2.4 Loading EVLA data in CASA
 4.3 Preparing for Calibration
  4.3.1 System Temperature Correction
  4.3.2 Antenna Gain-Elevation Curve Calibration
  4.3.3 Atmospheric Optical Depth Correction
   4.3.3.1 Determining opacity corrections for EVLA data
   4.3.3.2 Determining opacity corrections for VLA data
  4.3.4 Setting the Flux Density Scale using (setjy)
   4.3.4.1 Using Calibration Models for Resolved Sources
  4.3.5 Correction for delay and antenna position offsets using gencal
  4.3.6 Applying EVLA switched power or ALMA Tsys using gencal
  4.3.7 Other a priori Calibrations and Corrections
 4.4 Solving for Calibration — Bandpass, Gain, Polarization
  4.4.1 Common Calibration Solver Parameters
   4.4.1.1 Parameters for Specification : vis and caltable
   4.4.1.2 Selection: field, spw, selectdata, intent, and observation
   4.4.1.3 Prior Calibration and Correction: parang, gaincurve and opacity
   4.4.1.4 Previous Calibration: gaintable, gainfield, interp and spwmap
   4.4.1.5 Solving: solint, combine, preavg, refant, minblperant, minsnr
   4.4.1.6 Action: append and solnorm
  4.4.2 Spectral Bandpass Calibration (bandpass)
   4.4.2.1 Bandpass Normalization
   4.4.2.2 B solutions
   4.4.2.3 BPOLY solutions
  4.4.3 Complex Gain Calibration (gaincal)
   4.4.3.1 Polarization-dependent Gain (G)
   4.4.3.2 Polarization-independent Gain (T)
   4.4.3.3 GSPLINE solutions
   4.4.3.4 Antenna Delays — ’K’ solutions
   4.4.3.5 Cross-Hand Delays — ’KCROSS’ solutions
  4.4.4 Establishing the Flux Density Scale (fluxscale)
   4.4.4.1 Using Resolved Calibrators
  4.4.5 Instrumental Polarization Calibration (D,X)
   4.4.5.1 Heuristics and Strategies for Polarization Calibration
   4.4.5.2 A Note on channelized polarization calibration
   4.4.5.3 A Polarization Calibration Example
  4.4.6 Baseline-based Calibration (blcal)
 4.5 Plotting and Manipulating Calibration Tables
  4.5.1 Plotting Calibration Solutions (plotcal)
   4.5.1.1 Examples for plotcal
  4.5.2 Listing calibration solutions with (listcal)
  4.5.3 Calibration table statistics (calstat)
  4.5.4 Calibration Smoothing (smoothcal)
  4.5.5 Calibration Interpolation and Accumulation (accum)
   4.5.5.1 Interpolation using (accum)
   4.5.5.2 Incremental Calibration using (accum)
 4.6 Application of Calibration to the Data
  4.6.1 Application of Calibration (applycal)
  4.6.2 Examine the Calibrated Data
  4.6.3 Resetting the Applied Calibration using (clearcal)
 4.7 Other Calibration and UV-Plane Analysis Options
  4.7.1 Splitting out Calibrated uv data (split)
   4.7.1.1 Averaging in split
  4.7.2 Recalculation of uvw values (fixvis)
  4.7.3 Hanning smoothing of uv data (hanningsmooth)
  4.7.4 Model subtraction from uv data (uvsub)
  4.7.5 UV-Plane Continuum Subtraction (uvcontsub)
  4.7.6 Spectral regridding of the MS (cvel)
  4.7.7 UV-Plane Model Fitting (uvmodelfit)
 4.8 Examples of Calibration
5 Synthesis Imaging
 5.1 Imaging Tasks Overview
 5.2 Common Imaging Task Parameters
  5.2.1 Parameter cell
  5.2.2 Parameter field
  5.2.3 Parameter imagename
  5.2.4 Parameter imsize
  5.2.5 Parameter mode
   5.2.5.1 Mode mfs
   5.2.5.2 Mode channel
   5.2.5.3 Mode frequency
   5.2.5.4 Mode velocity
   5.2.5.5 Sub-parameter interpolation
  5.2.6 Parameter phasecenter
  5.2.7 Parameter restfreq
  5.2.8 Parameter spw
  5.2.9 Parameter stokes
  5.2.10 Parameter uvtaper
  5.2.11 Parameter weighting
   5.2.11.1 ’natural’ weighting
   5.2.11.2 ’uniform’ weighting
   5.2.11.3 ’superuniform’ weighting
   5.2.11.4 ’radial’ weighting
   5.2.11.5 ’briggs’ weighting
   5.2.11.6 ’briggsabs’ weighting
  5.2.12 Parameter vis
  5.2.13 Primary beams in imaging
 5.3 Deconvolution using CLEAN (clean)
  5.3.1 Parameter psfmode
   5.3.1.1 The clark algorithm
   5.3.1.2 The hogbom algorithm
   5.3.1.3 The clarkstokes algorithm
  5.3.2 The multiscale parameter
  5.3.3 Parameter gain
  5.3.4 Parameter imagermode
   5.3.4.1 Sub-parameter cyclefactor
   5.3.4.2 Sub-parameter cyclespeedup
   5.3.4.3 Sub-parameter ftmachine
   5.3.4.4 Sub-parameter mosweight
   5.3.4.5 Sub-parameter scaletype
   5.3.4.6 The threshold revisited
  5.3.5 Parameter interactive
  5.3.6 Parameter mask
   5.3.6.1 Setting clean boxes
   5.3.6.2 Using clean mask images
  5.3.7 Parameter minpb
  5.3.8 Parameter modelimage
  5.3.9 Parameter niter
  5.3.10 Parameter pbcor
  5.3.11 Parameter restoringbeam
  5.3.12 Parameter threshold
  5.3.13 Parameter gridmode
  5.3.14 Interactive Cleaning — Example
  5.3.15 Mosaic imaging
  5.3.16 Heterogeneous imaging
  5.3.17 Polarization imaging
  5.3.18 Wide-field imaging and deconvolution in clean
   5.3.18.1 Outlier fields
   5.3.18.2 Setting up w-projection
   5.3.18.3 Setting up faceting
   5.3.18.4 Combination of w-projection and faceting
 5.4 Primary Beam Correction (impbcor)
 5.5 Combined Single Dish and Interferometric Imaging (feather)
 5.6 Making Deconvolution Masks or Box Regions
  5.6.1 Making Deconvolution Regions from an Image (boxit)
 5.7 Transforming an Image Model (ft)
 5.8 Image-plane deconvolution (deconvolve)
 5.9 Self-Calibration
 5.10 Examples of Imaging
6 Image Analysis
 6.1 Common Image Analysis Task Parameters
  6.1.1 Region Selection (box)
  6.1.2 Plane Selection (chans, stokes)
  6.1.3 Lattice Expressions (expr)
  6.1.4 Masks (mask)
  6.1.5 Regions (region)
 6.2 Image Header Manipulation (imhead)
  6.2.1 Examples for imhead
 6.3 Continuum Subtraction on an Image Cube (imcontsub)
  6.3.1 Examples for imcontsub)
 6.4 Image-plane Component Fitting (imfit)
  6.4.1 Examples for imfit
 6.5 Mathematical Operations on an Image (immath)
  6.5.1 Examples for immath
   6.5.1.1 Simple math
   6.5.1.2 Polarization manipulation
  6.5.2 Using masks in immath
 6.6 Computing the Moments of an Image Cube (immoments)
  6.6.1 Hints for using (immoments)
  6.6.2 Examples using (immoments)
 6.7 Computing image statistics (imstat)
  6.7.1 Using the task return value
  6.7.2 Examples for imstat
 6.8 Extracting data from an image (imval)
 6.9 Reordering the Axes of an Image Cube (imtrans)
 6.10 Collapsing an Image Along an Axis (imcollapse)
 6.11 Regridding an Image (imregrid)
 6.12 Image Convolution(imsmooth)
 6.13 Spectral Line fitting with specfit
 6.14 Search for Spectral Line Rest Frequencies (slsearch)
 6.15 Convert Exported Splatalogue Catalogs to CASA Tables (splattotable)
 6.16 Image Import/Export to FITS
  6.16.1 FITS Image Export (exportfits)
  6.16.2 FITS Image Import (importfits)
 6.17 Using the CASA Toolkit for Image Analysis
 6.18 Examples of CASA Image Analysis
7 Visualization With The CASA Viewer
 7.1 Starting the viewer
  7.1.1 Running the CASA viewer outside casapy
 7.2 The viewer GUI
  7.2.1 The Viewer Display Panel
  7.2.2 Saving and Restoring Display Panel State
  7.2.3 Region Selection and Positioning
  7.2.4 The Load Data Panel
   7.2.4.1 Registered vs. Open Datasets
 7.3 Viewing Images
  7.3.1 Viewing a raster map
   7.3.1.1 Raster Image — Display Axes
   7.3.1.2 Raster Image — Basic Settings
   7.3.1.3 Raster Image — Other Settings
  7.3.2 Viewing a contour map
  7.3.3 Overlay contours on a raster map
  7.3.4 Spectral Profile Plotting
  7.3.5 Managing and Saving Regions
  7.3.6 Adjusting Canvas Parameters/Multi-panel displays
   7.3.6.1 Setting up multi-panel displays
   7.3.6.2 Background Color
 7.4 Viewing Measurement Sets
  7.4.1 Data Display Options Panel for Measurement Sets
   7.4.1.1 MS Options — Basic Settings
   7.4.1.2 MS Options— MS and Visibility Selections
   7.4.1.3 MS Options — Display Axes
   7.4.1.4 MS Options — Flagging Options
   7.4.1.5 MS Options— Advanced
   7.4.1.6 MS Options — Apply Button
 7.5 Printing from the Viewer
 7.6 Image Viewer (imview)
 7.7 Measurement Viewer (msview)
8 Single Dish Data Processing
 8.1 Guidelines for Use of ASAP and SDtasks in CASA
  8.1.1 Environment Variables
  8.1.2 Assignment
  8.1.3 Lists
  8.1.4 Dictionaries
  8.1.5 Line Formatting
  8.1.6 Logging
 8.2 Single Dish Analysis Tasks
  8.2.1 SDtask Summaries
   8.2.1.1 sdaverage
   8.2.1.2 sdsmooth
   8.2.1.3 sdbaseline
   8.2.1.4 sdcal
   8.2.1.5 sdcoadd
   8.2.1.6 sdflag
   8.2.1.7 sdflagmanager
   8.2.1.8 sdfit
   8.2.1.9 sdimaging
   8.2.1.10 sdlist
   8.2.1.11 sdmath
   8.2.1.12 sdplot
   8.2.1.13 sdsave
   8.2.1.14 sdscale
   8.2.1.15 sdstat
   8.2.1.16 sdtpimaging
   8.2.1.17 sdimprocess
   8.2.1.18 msmoments
  8.2.2 Single Dish Analysis Use Cases With SDTasks
   8.2.2.1 GBT Position Switched Data Analysis
   8.2.2.2 Imaging of Total Power Raster Scans
 8.3 Using The ASAP Toolkit Within CASA
  8.3.1 Environment Variables
  8.3.2 Import
   8.3.2.1 General descriptions
   8.3.2.2 Handling ALMA data
  8.3.3 Scantable Manipulation
   8.3.3.1 Data Selection
   8.3.3.2 State Information
   8.3.3.3 Masks
   8.3.3.4 Scantable Management
   8.3.3.5 Scantable Mathematics
   8.3.3.6 Scantable Save and Export
  8.3.4 Calibration
   8.3.4.1 Tsys scaling
   8.3.4.2 Flux and Temperature Unit Conversion
   8.3.4.3 Gain-Elevation and Atmospheric Optical Depth Corrections
   8.3.4.4 Calibration of GBT data
   8.3.4.5 Comprehensive calibration function
  8.3.5 Averaging
  8.3.6 Spectral Smoothing
  8.3.7 Baseline Fitting
  8.3.8 Line Fitting
  8.3.9 Plotting
   8.3.9.1 ASAP plotter
   8.3.9.2 Line Catalog
  8.3.10 Setting/Getting Rest Frequencies
  8.3.11 Single Dish Spectral Analysis Use Case With ASAP Toolkit
 8.4 Single Dish Imaging
  8.4.1 Single Dish Imaging Use Case With ASAP Toolkit
 8.5 Known Issues, Problems, Deficiencies and Features
9 Simulation
 9.1 Simulating ALMA with simdata
10 Parallel Processing in CASA
A Appendix: Obtaining, Installing, and Customizing CASA
 A.1 Installation On Linux
  A.1.1 Installation
  A.1.2 Unsupported platforms
  A.1.3 Download & Unpack
 A.2 Installation on Mac OS
 A.3 Startup
 A.4 Startup Customization
B Appendix: Python and CASA
 B.1 Automatic parentheses
 B.2 Indentation
 B.3 Lists and Ranges
 B.4 Dictionaries
  B.4.1 Saving and Reading Dictionaries
 B.5 Control Flow: Conditionals, Loops, and Exceptions
  B.5.1 Conditionals
  B.5.2 Loops
 B.6 System shell access
  B.6.1 Using the os.system methods
  B.6.2 Directory Navigation
  B.6.3 Shell Command and Capture
 B.7 Logging
 B.8 History and Searching
 B.9 Macros
 B.10 On-line editing
 B.11 Executing Python scripts
 B.12 How do I exit from CASA?
C Appendix: Models, Conventions and Reference Frames
 C.1 Flux Density Models for setjy
  C.1.1 Long wavelength calibration
   C.1.1.1 Baars
   C.1.1.2 Perley 90
   C.1.1.3 Perley-Taylor 95
   C.1.1.4 Perley-Taylor 99
   C.1.1.5 Perley-Butler 2010
  C.1.2 Short wavelength calibration
  C.1.3 References to this Section
 C.2 Velocity Reference Frames
  C.2.1 Doppler Types
 C.3 Time Reference Frames
 C.4 Coordinate Framess
 C.5 Physical Units
 C.6 Physical Constants
D Appendix: CASA Region File Format
 D.1 Region definitions
 D.2 Allowed shapes
 D.3 Annotation definitions
 D.4 Global definitions
 D.5 Allowed additional parameters
 D.6 Examples
 D.7 Fonts and Symbols
  D.7.1 Allowed symbols
  D.7.2 Allowed fonts
   D.7.2.1 Allowed fonts for Linux
   D.7.2.2 Allowed fonts for MacOS X
E Appendix: The Measurement Equation and Calibration
 E.1 The HBS Measurement Equation
 E.2 General Calibrater Mechanics
F Appendix: Annotated Example Scripts
 F.1 NGC 5921 — VLA red-shifted HI emission
 F.2 Jupiter — VLA continuum polarization
 F.3 BIMA Mosaic Spectral Imaging
G Appendix: CASA Dictionaries
 G.1 AIPS – CASA dictionary
 G.2 MIRIAD – CASA dictionary
 G.3 CLIC – CASA dictionary
H Appendix: Writing Tasks in CASA
 H.1 The XML file
 H.2 The task_yourtask.py file
 H.3 Example: The clean task
  H.3.1 File clean.xml
  H.3.2 File task_clean.py

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