CASA Beta Release Notes (Beta Patch 4)

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CASA Beta Release Notes:

Valid for Beta patch 4.0 (CASA Version 2.4.0) and later.

What's New in Beta Patch 4.0 (CASA Version 2.4.0)

The Beta Release Patch 4 includes the following changes:

New interface changes:

The AIPSPATH environment variable is now the CASAPATH variable.
If you type help task without quotes around the task name, you will get two copies of the help with alot of extraneous stuff. This is a bug introduced in 2.4.0 and will be fixed in later releases.

New data handling features:

A number of importvla improvements were made:
1. In previous releases, importvla did not provide a valid DOPPLER subtable. This has been fixed in 2.4.0. release.
2. The keepblanks parameter is defaulted to False, so tipping scans will not be included in the measurement set. Setting this to True will include the tipping scans.
3. Data edited as having zero weight are now flagged, instead of simply being carried around with a weight of 0. This fixes an issue in the viewer where existing flags were ignored while performing additional flagging.
4. VLA antennas are now sorted into numerical (name) order, and the station naming has been enhanced to include the VLA/EVLA distinction.
5. Duplicate field names for different source positions in the archive (a rare occurence) are resolved with an appended digit to permit selecting such fields uniquely in subsequent processing.
The task importuvfits has a new parameter antnamescheme (as in importvla) which when set to 'new' and you are importing VLA data, then it will prepend either VA or EV to the antenna name.
Data can be compressed in importasdm by setting compression = True.
The concat task now has a timesort parameter to trigger time-based resorting of the output MS.
A number of changes to listobs output, including reporting of rest frequency and velocity information, integration time, source identification, time frame.
There is a prototype vishead task that allows the user to manipulate some common metadata items in a measurement set (e.g. to list, get, and put values).
A new task called rmtables has been created to cleanly remove tables. This helps if the user is trying to process data (e.g. an image) from scratch, and not continue from a previous session. It will not remove things that have open handles.

New plotting and flagging features:

A number of changes were made to flagdata:
1. The task now has the feature where some parameters can take lists, so only one invocation of the task can apply any number of flagging specification
2. The task now uses the standard selectdata parameters.
3. The correlation sub-parameter now takes more options, e.g. 'RR LL', 'RR,LL', etc.
4. The mode parameter now has a 'shadow' option.
The task plotants now has the capability to save a plot as a file (parameter figfile).
There is a new prototype MS plotting application casaplotms. This is experimental and under active development, and is not yet integrated into casapy (is a standalone application).

New synthesis calibration features:

There are models for 3C147 at C and X band now available in setjy.
In the calibration tasks, there is now a minblperant parameter, which enables the user to control the minimum number of baselines required for an antenna to be solved for.
The task split can now go directly from a multi SPW measurement set to a time averaged one with the same set of SPWs, and/or split to a single SPW at the same time.
The split task can now do frequency averaging then time averaging consecutively with no issues.
The split task datacolumn parameter now takes options 'data', 'corrected', 'model', 'all'.

New synthesis imaging features:

A number of clean improvements were made:
1. The mode parameter has a new sub-parameter interpolation to control how data is gridded onto the spectral cube axis in channel, velolcity, and frequency modes. This has 3 possible values: `nearest', `linear', and `cubic'.
2. There were a number of cosmetic and fuctional changes made to the interactive clean viewer panel.
3. In clean if you are reducing data from a telescope whose beam is not found in the list of known arrays in CASA, the dish diameter (found in the antenna table) is used to scale an Airy disk pattern beam.
4. Option stokes = 'IQU' is now available.
5. The psfmode settings 'hogbom' does sequential cleaning while 'clark' and 'csclean' do joint convolution.
6. For imagermode='mosaic' the minpb parameter now cuts the imaging off at the specified level in the unweighted primary-beam coverage, as reflected in the new output image <imagename>.flux.pbcoverage.

New image analysis features:

All of the WCS projections for FITS images described in the FITS standard v3.0 are now supported by CASA. CASA will read and write standard-compliant FITS images. FITS image files that are not WCS compliant are accepted by applying a dummy linear coordinate along each axis.
In FITS images, all brightness units complying with the FITS standard v3.0 are recognized. Non-recognized units are accepted and treated as "non-dimensional". The unit maps in quanta and the FITS unit add-on were extended to cover the FITS standard v3.0.
There is a new task called imsmooth that will smooth images in the spectral and XY planes.
All of the image analysis tasks (imstat, imval, etc.) with the region parameter have been updated to take as input: region file name saved by the viewers region manager, region name stored with the image given by imagename, region in any image with the syntax image_filename:region_name.

New viewer features:

The viewer Maximum Contour slider has been replaced with the Unit Contour slider, found under basic settings .
The region manager on the viewer has changed, and you can now save regions with an image file and/or on disk.

New single-dish processing features:

The sdfit task now has the capability to plot the whole spectral region to see the entire spectral shape when the fitted result is verified.
In the sdbaseline and sdcal tasks the parameter interactive has been renamed as verify.
In the sdcal task interactive mask selection is enabled with blmode = 'interact'.
It is now possible in sdplot to get statistics by selecting a region with mouse button on a plot displayed by the task.
There are a number of other changes, as this CASA module is under continuous development. See the Appendix A of the Cookbook for the latest guide.

New simulator features:
1. The simulator task is now called simdata (used to be almasimmos). This task has many new features. See Appendix B of the Cookbook, and the for more info.

Previous Versions

Fixes in Beta Patch 3.1 (CASA Version 2.3.1)

This is an incremental update for 2.3.0.

Fixes in Beta Patch 3.0 (CASA Version 2.3.0)

The updated Beta Release Patch 3 includes the following changes:

The versioning of CASA has changed such that the startup and casalog.version now report Version X.Y.Z where X=2 for the Beta Release, Y is the Patch number, and Z is the sub-patch release. For example, the December 2008 Patch 3.0 release is Version 2.3.0.
In plotxy the user can extend the flagging in various ways by setting extendflag=T and then setting one or more sub-parameters. This allows data other than that shown to be flagged along with the marked data (e.g. extending flags to all correlation products).
The bandtype='BPOLY' option now has the capability of getting solutions in different sets of spectral windows whem combine='spw' is on.
There is now a widefield prototype task to make wide-field (e.g. low frequency) images using w-projection and/or faceting. Includes the ability to image multiple flanking fields set up using a box file.
The clean task now handles multiple dish sizes for heterogeneous imaging.
There is now a imval task that will return the data values in an image at a given pixel or in a specified region.
The imfit task has improved reporting of fit results.
The viewer now has the option to Save and Restore Panel Settings using an option from the Data menu.
There is now a buildmytasks facility in CASA that allows users to create a new task or modify an existing one and use it. See Appendix H of the Cookbook for more information.

Fixes in Beta Patch 2.2

The updated Beta Release Patch 2.2 for Linux includes the following fixes to Patch 2.1:

At startup, the plotter display (used by plotxy and plotcal are now correctly initialized under 64-bit systems. Symptoms were that the plotter would appear but did not work interactively for some 64-bit OS.

Fixes in Beta Patch 2.1

The updated Beta Release Patch 2.1 includes the following fixes to Patch 2.0:

A fix to the clean task to catch an error introduced by the importvla filler on some VLA line datasets (such as the NGC2403 script) where the Doppler subtable has an incorrect index;
Use of an updated matplotlib library which fixes some memory leaks.
A bug was introduced in the original Patch 2.1 MacOSX distribution dated 25-Jul-2008 where the viewer would not start up from within casapy. This was fixed in the .dmg posted on 28-July-2008. If you have the earlier version, please download and install the updated one!

What's New in Beta Patch 2.0

There are a number of new and/or improved features available in Patch 2.0:

Support for additional Linux architectures (see below), including: SuSE, Ubuntu, Debian;
Significant interface changes (see Cookbook Chapter 1), including:
- tasks no longer set global variables (e.g. on execution),
- global CASA parameters are not used when tasks are called with arguments (e.g. plotxy('ngc5921.ms')), only when invoked with go or without arguments (e.g. plotxy()),
- removal of output parameters from those that used them (imhead, imstat, sdstat), these now use return values, e.g. xstat=imstat();
Improvements to Data I/O tasks and data handling (see Cookbook Chapter 2), including:
- Improvements in the ASDM filler importasdm (e.g. updated to latest ASDM format and code),
- ATA, BIMA, and SMA observatory (e.g. primary beam) info in system repository;
Improvements to plotxy (see Cookbook Chapter 3), including:
- Various bugs fixes (e.g. bogus points no longer plotted, showflags, antenna iteration, some of the averaging issues),
- Can now plot xaxis='velocity',
- Vector averaging across baselines (crossbls=T);
Improvements to Synthesis Calibration tasks (see Cookbook Chapter 4), including:
- Addition of a combine parameter to many calibration tasks, allowing calibration solutions to cross scan, field and spw boundaries (not currently used for GSPLINE and BPOLY solutions);
- The behavior of the solint parameter has changed such that solint=0 gives per-integration solutions (used to give per-scan solutions). It now also takes a string, which can be a time quantity or the special values 'inf' (all times) or 'int' (per integration). To get scan-based solutions, set solint='inf' and combine='' (to not cross scans). WARNING: your scripts from Patch1 and earlier may need to be changed.
- The uvcontsub task now uses the new solint parameter changes (see above).
Improvements to Synthesis Imaging tasks (see Cookbook Chapter 5), including:
- Major rework of clean task, which now contains the functionality of mosaic and invert as well (see in-line help clean for parameters and options),
- clean now produces .psf and .flux images by default,
- Interactive cleaning improved (e.g more values persistent, default is to apply the mask to the current plane instead of not all),
- The PSF at the center of the nearest field to the phase center is now used,
- Bug in mosaic flux scaling when a PB was not at the phase center was fixed,
- Output image is now fully masked outside the PB cutoff;
Additions and improvements to Image Analysis tasks (see Cookbook Chapter 6), including:
- new task imfit - fit a single Gaussian to an image;
- improved imhead - list option now returns a record;
- improved immath - options for spectral index, intensity and angle;
- the Lattice Expression Language (LEL) in the image analysis tasks and tools is now fully 0-based, while previously it was partly 1-based. This is most noticeable in the immoments task with the planes parameter, and in using the INDEXIN LEL function;
Viewer improvements (see Cookbook Chapter 7), including:
- Pixel and World coordinates always both displayed in the Position Tracking panel,
- The abiity for MS raster plotting to sort baselines by baseline length,
- "On the fly" image mathematics are available in the Open panel as a box for LEL. This can be used to avoid running immath and leaving lots of temporary images on disk),
- The ability to write the single most recent polygon/box region to a file. for easier use in image tasks (e.g. immath)
Single dish improvements (see Cookbook Appendix A), including:
- polarization support, parameter consistency;
An improved ALMA simulator almasimmos (see Cookbook Appendix B), and ALMA Simulator Wiki), including:
- much better display, noise generation;
Other task improvements, including:
- concat now makes new dataset, takes in many input datasets,
- listcal and listvis improvements (e.g. crosses channels and spectral windows, lists all bandpass channels),
- new plotter available in browsetable;
more comprehensive history information from task processing included in MS history table;
Toolkit documentation in the User Reference Manual is in the process of being re-edited and brought up to date, (e.g. Glish references removed from most pages);
sundry bug fixes.

Supported Platforms

Note that the Beta Release is only available for a limited number of supported platforms and OS:

Red Hat Enterprise Linux 4 and 5 (32 and 64 bit)
Red Hat Fedora Core 6, 7 and 8 (32 bit only)
Macintosh OSX (for Intel Macs, versions 10.4.7 and later, 32 bit only)
openSuSE 10.0, 11.0 (32 and 64 bit)
Ubuntu 8.0.4 (32 and 64 bit)
Debian 4.0 (32 and 64 bit)

Science Scope

The Beta Release is aimed at supporting basic interferometric data reduction. It will support the import of data in a limited number of formats, and a reasonably full set of processing capabilities for only a limited number of observing modes. These are:

WILL support data from:

VLA, for frequencies > 1.3 GHz (except L-band A-configuration, no wide-field imaging), in the formats:

Archive
UVFITS (e.g. written via AIPS FITTP)

other telescopes, in UVFITS (e.g. compatible with AIPS FITLD/FITTP)
(The ASDM filler is currently being installed by the ALMA project directly at ALMA operational sites since it is being updated rapidly now that ASDM data is being generated/debugged at the ALMA Test Facility at the VLA site. It will be redistributed with CASA in subsequent patches.
See full data import facilities here
WILL support observing modes:
- single field interferometry
- simple mosaics
- simple combination of a single-dish image with interferometry
- polarimetry

For more information, see the Beta Release Known Issues and FAQ page.

Functionality

A set of tasks are available for basic reduction/analysis needs:

Available tasks: 

Import/Export    Information  Data Editing  Display/Plot
-------------    -----------  ------------  ------------
importvla        listcal      (fixvis)      clearplot
(importasdm)     listhistory  flagautocorr  plotants 
importfits       listobs      flagdata      plotcal
importuvfits     listvis      flagmanager   plotxy
exportfits       imhead       plotxy        viewer
exportuvfits     imstat
                 vishead

Calibration      Imaging      Modelling     Utility
-----------      -------      ---------     -------
accum            clean        setjy         help task
applycal         deconvolve   uvcontsub     help par.parameter
bandpass         feather      (uvcontsub2)  taskhelp
blcal            ft           uvmodelfit    tasklist
gaincal          invert                     browsetable
fluxscale        makemask                   clearplot
(fringecal)      mosaic                     clearstat
clearcal         (widefield)                concat
listcal                                     filecatalog
smoothcal                                   startup
polcal                                      split
hanningsmooth                               fixvis
                                                 

Image Analysis   Simulation   Single Dish
--------------   ----------   -----------
imcontsub        simdata      sdaverage
imhead                        sdbaseline
immath                        sdcal
immoments                     sdcoadd
imregrid                      sdfit
imsmooth                      sdflag
imstat                        sdlist
imval                         sdplot
(specfit)                     sdsave
                              sdscale
                              sdsmooth
                              sdstat

accum : Accumulate incremental calibration solutions into a calibration table
applycal : Apply calibrations solutions(s) to data
bandpass : Calculates a bandpass calibration solution
blcal : Calculate a baseline-based calibration solution (gain or bandpass)
browsetable : Browse a table (MS, calibration table, image)
clean : Deconvolve an image with selected algorithm
clearcal : Re-initializes the calibration for a visibility data set
clearplot : Clear the matplotlib plotter and all layers
clearstat : Clear all read/write locks
concat : Concatenate two visibility data sets.
deconvolve : Image based deconvolver
exportfits : Convert a CASA image to a FITS file
exportuvfits : Convert a CASA visibility data set to a UVFITS file:
feather : Feathering: Combine two images using the Fourier Addition
find : Find string in tasks, task names, parameter names:
flagautocorr : Flag autocorrelations
flagdata : All purpose flagging task based on selections
flagmanager : Enable list, save, restore and delete flag version files.
fluxscale : Bootstrap the flux density scale from standard calibrators
fringecal : Calculate a baseline-based fringe-fitting solution
ft : Insert a source model into the MODEL_DATA column of a MS
gaincal : Determine temporal gains from calibrator observations
hanningsmooth : Hanning smooth frequency channel data to remove Gibbs ringing
imcontsub : Subtracts specified continuum channels from a spectral line dataset
imfit : Fit One Elliptical Gaussian Component on an image region(s)
imhead : List, get and put image header parameters
immath : Perform math operations on images
immoments : Compute moments from an image
importasdm : Convert an ALMA Science Data Model observation into a CASA visibility file
importfits : Convert an image FITS file into a CASA image
importuvfits : Convert a UVFITS file to a CASA visibility data set
importvla : Import VLA archive file(s) to a measurement set
imregrid : regrid an image onto a template image
imstat : Displays statistical information from an image or image region
imval : Get the data value(s) and/or mask value in an image
listcal : List calibrated antenna gain solutions
listhistory : List the processing history of a dataset:
listobs : List data set summary in the logger
listvis : List measurement set visibilities.
makemask : Derive a mask image from a cleanbox blc, trc regions
plotants : Plot the antenna distribution in the local reference frame:
plotcal : An all-purpose plotter for calibration results
plotxy : X-Y plotter/interactive flagger for visibility data
polcal : Determine instrumental polarization calibrations
sdaverage : ASAP SD task: do data selection, calibration, and averaging
sdbaseline : ASAP SD task: fit/remove a spectral baseline
sdcal : ASAP SD task: do sdaverage, sdsmooth, and sdbaseline in one task
sdcoadd : ASAP SD task: coadd multiple scantables into one
sdfit : ASAP SD task: fit a spectral line
sdflag : ASAP SD spectral flagging task
sdlist : ASAP SD task: list summary of single dish data
sdplot : ASAP SD plotting task
sdsave : ASAP SD task: save the sd spectra in various format
sdscale : ASAP SD task: scale the sd spectra
sdsmooth : ASAP SD task: do smoothing of spectra
sdstat : ASAP SD task: list statistics of spectral region
sdtpimaging : SD task: do a simple calibration and imaging for total power data
setjy : Set the flux scale using standard source fluxes or models
simdata : simulation task (prototype):
smoothcal : Smooth calibration solution(s) derived from one or more sources:
specfit : Fit 1-dimentional profile(s) or polynomial(s) to an image or image region
split : Write new MS with selection and/or averaging
uvcontsub : Continuum fitting and subtraction in the uv plane
uvcontsub2 : (prototype for replacement of uvcontsub)
uvmodelfit : Fit a single component source model to the uv data
uvsub : Subtract/add model from/to the corrected visibility data.
viewer : View an image or visibility data set:
viewer : View an image or visibility data set:
vishead : List, summary, get, and put metadata in a measurement set
widefield : Wide-field imaging and deconvolution with selected algorithm

Please send any comments or questions about CASA to casa-request@nrao.edu

This code is available under the terms of the GNU General Public Lincense

Copyright © 2009 Associated Universities, Inc.
The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.

Modified on Wednesday, 24-Jun-2009 10:21:55 MDT