1. Introduction to CASA and Basic Data Reduction Overview Crystal Brogan ALMA CASA Subsystem Scientist (NRAO/NAASC) With lots of help from Steve Myers (Project Scientist) http://www.cv.nrao.edu/~cbrogan/CASATutorial_Santiago.pdf

2. CASA Tutorial – Santiago Jan. 26, 2009 2 Beta Release Status CASA Status: in Beta Release since October 2007 Roughly biannual “patches” register at my.nrao.edu, no password for download Current Release: Beta Release Patch 2.3.1 Next Release @June ‘09

3. CASA Tutorial – Santiago Jan. 26, 2009 3 Getting User Support First stop: Read the Manual! CASA Home: http://casa.nrao.eduhttp://casa.nrao.edu Cookbook, and “help” within CASA CASA Helpdesk & Support Cadres “Helpdesk” under my.nrao.edu (will migrate to more user friendly helpdesk in future) submit Issues

4. CASA Tutorial – Santiago Jan. 26, 2009 Other Information 4 Some ALMA User software demos: almasimmos OT, and splatalogue: http://www.cv.nrao.edu/~jstoke/Demo_Videos/ The Eleventh Synthesis Imaging Workshop: Calibration, Imaging, Mosaicing, Millimeter Interferometry etc.: http://www.aoc.nrao.edu/events/synthesis/2008/le ctures08.html

5. CASA Tutorial – Santiago Jan. 26, 2009 5 CASA Documentation CASA Analysis cookbook (draft): http://casa.nrao.edu/Doc/Draft/Cookbook/casa_cookbook.pdf CASA User Reference Manual: http://casa.nrao.edu/docs/casaref/CasaRef.html Python: http://python.orghttp://python.org/doc (e.g., see Tutorial for novices) IPython: http://ipython.scipy.org/moin/Documentation matplotlib: http://matplotlib.sourceforge.nethttp://matplotlib.sourceforge.net/

6. CASA Tutorial – Santiago Jan. 26, 2009 6 Tutorial Contents I - Interface II - Tasks & Tools III - Data in CASA IV - Data Processing Workflow V - Example Use Cases

7. CASA Tutorial – Santiago Jan. 26, 2009 7 I - Interface Documentation IPython & Python Crashes & Recovery CASA help CASA task interface Functionality

8. CASA Tutorial – Santiago Jan. 26, 2009 8 I - CASA Interface IPython shell access autoparenthesis (autocall) command history session logging (ipython.log, casapy.log) numbered input/output history/searching Python see standard manuals, Cookbook Appendix D

9. CASA Tutorial – Santiago Jan. 26, 2009 9 Python Pointers to run a.py script: execfile(‘ ’) example: execfile(‘ngc5921_demo.py’) indentation matters! be careful when doing cut-and-paste to Python cut a few (4-6) lines at a time variables are global when using task interface! tasknames are objects (not variables)

10. CASA Tutorial – Santiago Jan. 26, 2009 10 Part II - Tasks & Tools overview of tasks and tools in CASA introduction to the task interface how to get help on tasks and tools how tools underly the tasks how to run tasks asynchronously

11. CASA Tutorial – Santiago Jan. 26, 2009 11 Tasks and tools in CASA Tasks - high-level functionality function call or parameter handling interface these are what you should use in tutorial Tools - complete functionality tool.method calls, used by tasks sometimes shown in tutorial scripts

12. CASA Tutorial -- 7 October 2008 Key Tasks Task list: may be different in test and release versions asap_init to load single-dish tasks and tools

13. CASA Tutorial – Santiago Jan. 26, 2009 13 Task Execution two ways to invoke: call from Python as functions with arguments taskname( arg1=val1, arg2=val2,... ) unspecified parameters will be defaulted (globals not used) use standard tasking interface use global variables for task parameters see Chapter 1.3 in Cookbook

14. CASA Tutorial – Santiago Jan. 26, 2009 14 Task Interface standard tasking interface use parameters set as global Python variables set = (e.g. vis = ‘ngc5921.demo.ms’ ) parameter manipulation commands using inp, default, saveinputs, tget execute or go ( e.g. clean() ) return values some tasks return Python dictionaries, e.g. myval=imval()

15. CASA Tutorial – Santiago Jan. 26, 2009 15 Task Interface examine task parameters with inp :

16. CASA Tutorial – Santiago Jan. 26, 2009 16 Expandable Parameters boldface parameter are expandable

17. CASA Tutorial – Santiago Jan. 26, 2009 17 Parameter Checking sanity checks of parameters in inp : erroneous values in red

18. CASA Tutorial – Santiago Jan. 26, 2009 18 Help on Tasks In-line help command:

19. CASA Tutorial – Santiago Jan. 26, 2009 19 Tools in CASA CASA Toolkit underneath tasks core AIPS++ code (mostly in C++) tools are functions call from casapy as. () default tool objects are pre-constructed e.g. imager (im), calibrater (cb), ms (ms), etc. (see toolhelp)

20. CASA Tutorial – Santiago Jan. 26, 2009 20 CASA Tool List list of default tools from toolhelp : tools described in the CASA User Reference Manual: http://casa.nrao.edu/docs/casaref/CasaRef.html

21. CASA Tutorial – Santiago Jan. 26, 2009 21 Asynchronous Tasks run tasks in background set parameter async=True runs as separate process use taskmanager tool (tm) to monitor (Cookbook Chapter 1.3.2) messages will appear in logger in the asynchronous order useful to avoid known problems (e.g. exportfits / importfits) cannot retrieve return values from async tasks

22. CASA Tutorial – Santiago Jan. 26, 2009 22 III - Data in CASA data in CASA are stored in tables interferometry data in Measurement Sets (MS) also tables for images and calibration tables formats and structures defined in CASA memos accessed through table and ms tools row and column structure is logical not physical

23. CASA Tutorial – Santiago Jan. 26, 2009 23 The Measurement Set the MS is a directory on disk the MAIN table in table.* files also contains sub-tables e.g. FIELD, SOURCE, ANTENNA, etc. sub-tables are sub-directories to copy must cp -rf to get contents WARNING: moving a MS can break cal-table dependencies

24. CASA Tutorial – Santiago Jan. 26, 2009 24 Example MS Example: ls ngc5921.usecase.ms ls ngc5921.usecase.ms/FIELD

25. CASA Tutorial – Santiago Jan. 26, 2009 25 MAIN Table Contents Example using task browsetable:

26. CASA Tutorial – Santiago Jan. 26, 2009 26 More MS Details often will refer to “rows” & “columns” rows = integrations in spectral windows columns = time, u, v, w, DATA, weights, etc. there are “scratch columns” created when needed - can bloat the MS but (usually) less space than scratch copy of MS! CORRECTED_DATA, MODEL_DATA, IMAGING_WEIGHTS

27. CASA Tutorial – Santiago Jan. 26, 2009 27 Data Selection standard MS selection syntax see Chapter 2.5 of CASA Cookbook syntax detailed in CASA Memo http://casa.nrao.edu/Memos/msselection/index.html

28. CASA Tutorial – Santiago Jan. 26, 2009 28 Selection Example standard selection parameters e.g. for task gaincal: field and spw common standard selections expandable selectdata with other selections as sub-parameters

29. CASA Tutorial – Santiago Jan. 26, 2009 29 Selection Syntax see Chapter 2.5 of Cookbook field - string with source name or field ID can use ‘*’ as wildcard, first checks for name, then ID example: field = ‘1331+305’ ; field = ‘3C*’ ; field = ‘0,1,4~5’ spw - string with specwindow ID plus channels use ‘:’ as separator of spw from optional channelization use ‘^’ as separator of channels from step/width example: spw = ‘0~2’ ; spw = ‘1:10~30’ ; spw = ‘2~5:5~54^5’

30. CASA Tutorial – Santiago Jan. 26, 2009 30 Selection Syntax see Chapter 2.5 of Cookbook antenna - string with antenna name or ID first check for name, then ID (beware VLA name 1-27, ID 0-26) example: antenna = ‘1~5,11’ ; antenna = ‘VA*’ timerange - string with date/time range specify ‘T0~T1’, missing parts of T1 default to T0, can give ‘T0+dT’ example: timerange = ‘2007/10/16/01:00:00~06:30:00’

31. CASA Tutorial – Santiago Jan. 26, 2009 31 IV - Reduction Philosophy data is imported into MS keep original DATA inviolate calibration is carried in cal-tables will discuss cal-table philosophy later imaging creates images from MS feed back model images for self-calibration

32. CASA Tutorial – Santiago Jan. 26, 2009 32 Data Philosophy Original data kept intact by default DATA (and WEIGHT) columns do not change in original MS user can use toolkit to mess with these also MS “scratch columns” are used used for adjusted data and model visibilities BETA: user must keep track ; Post-Beta: hide table and MS state

33. CASA Tutorial – Santiago Jan. 26, 2009 33 CASA Workflow Chart workflow: import examine / flag calibrate image analyze

34. CASA Tutorial – Santiago Jan. 26, 2009 34 Workflow Steps follow rough workflow path: import data (from UVFITS or archive formats) examine data and edit out bad visibilities calibrate data (through cal-tables) image data (various deconvolution methods) image and uv analysis (e.g. moments) data and image visualization (whenever needed)

35. CASA Tutorial – Santiago Jan. 26, 2009 35 Import Data see Chapter 2 of Cookbook task importuvfits UVFITS data (e.g. from AIPS) task importvla VLA “export” format (e.g. from archive) task importasdm ALMA data format (also EVLA eventually)

36. CASA Tutorial – Santiago Jan. 26, 2009 36 Data Examination see Chapter 3 of Cookbook task listobs list summary of MS task plotxy x-y line plots task browsetable (casabrowser outside casapy) Qt browser for tables (e.g. MS and images) casaviewer - view raster images of MS

37. CASA Tutorial – Santiago Jan. 26, 2009 37 Flagging see Chapter 3 of Cookbook task plotxy draw boxes around points and flag casaviewer ( task viewer ) draw boxes on raster and flag (modes similar to AIPS TVFLG) task flagdata - manual flagging, clipping, etc. task flagmanager - backup & restore flags

38. CASA Tutorial – Santiago Jan. 26, 2009 38 Task plotxy use plotxy for simple data plots & flagging before (left) and after (right) editing and calibration

39. CASA Tutorial – Santiago Jan. 26, 2009 39 Task plotxy interactive plotting and flagging averaging timebin, width (time & channel averaging) iteration iteration = ‘antenna’, ‘field’, ‘time’, ‘spw’ (or combinations) GUI controls buttons for MarkRegion, Flag, Unflag, Locate, Next, Quit plot options use subplot = yxn to set multi-panels (e.g. subplot=311) controls for fontsize, markersize, other options

40. CASA Tutorial – Santiago Jan. 26, 2009 40 Example inputs set up to plot amp vs. time

41. CASA Tutorial – Santiago Jan. 26, 2009 41 Editing Jupiter isolate blocks of bad data and remove single bad scan on Jupiter both spw, all antennas

42. CASA Tutorial – Santiago Jan. 26, 2009 42 MS viewing the casaviewer can handle MS (e.g. TVFLG)

43. CASA Tutorial – Santiago Jan. 26, 2009 43 Calibration see Chapter 4 of Cookbook prior calibration solving calibration table manipulation calibration table examination application to data

44. CASA Tutorial – Santiago Jan. 26, 2009 44 Calibration workflow: input dataset solving => tables incremental accumulation application

45. CASA Tutorial – Santiago Jan. 26, 2009 45 Calibration Tables calibration tables are exchanged between the calibration tasks:

46. CASA Tutorial – Santiago Jan. 26, 2009 46 Calibration Tasks prior calibration: setjy solvers: gaincal, bandpass, polcal, blcal, fringecal manipulation: plotcal, accum, smoothcal application: applycal, split other: uvcontsub, uvmodelfit

47. CASA Tutorial – Santiago Jan. 26, 2009 47 Parameterizations prior calibration: gaincurve: VLA-only for now opacity: single tau value (for now) gaincal: gaintype=’G’ (solution per solint time slot) gaintype=’GSPLINE’ bandpass: bandtype=’B’ (solution per channel) bandtype=’BPOLY’ No time-dependence yet

48. CASA Tutorial – Santiago Jan. 26, 2009 48 Calibration Processing setjy (or ft) specify a model image (for selfcal or resolved cals) Except for uv-range does not yet handle planets, VLA calibrator models are available smoothcal Mean, median smoothing of cal tables accum calibration re-sampling Incremental/cumulative calibration

49. CASA Tutorial – Santiago Jan. 26, 2009 49 Imaging see Chapter 5 of Cookbook task clean single-field cleaning, variety of algorithms mosaicing using uv-gridder (uv-plane mosaicing on single image) interactive and non-interactive operation task widefield - widefield imaging prototype w-projection and faceting task feather - combine single-dish and uvMS

50. CASA Tutorial – Santiago Jan. 26, 2009 50 Interactive CLEAN clean has interactive mode interactive=True uses the viewer can change cycles during cleaning draw boxes and polygon regions for masking

51. CASA Tutorial – Santiago Jan. 26, 2009 51 Cube Channelization When using mode=‘channel’ select spectral windows of the data, e.g. spw=‘0,1’ the width is then set in units of first data spw channel width

52. CASA Tutorial – Santiago Jan. 26, 2009 52 Imaging spectral cubes Other cube considerations... Averaging of data channel in imaging is always ‘mfs’ style…i.e gridded with different (u,v) If a mode=’velocity’ cube is chosen, then data will be gridded into LSRK bins If simple data averaging is needed split is recommended

53. CASA Tutorial – Santiago Jan. 26, 2009 53 Mosaicing in clean use imagermode=’mosaic’ deconvolution on “Sault” (constant noise) image User can set make PB corrected image at end Heterogeneous now available if multiple antenna diameters are present primary beam coverage x Sky in image plane Convolution with aperture cross-correlation function in uv-domain Advantages of doing mosaicing in uv Faster and apply correct beam transform for each baseline (e.g. different dish size, change of pb with frequency, beam errors etc.) Parameter “ ftmachine ” sets this Possibilities are ' ft ' or ' mosaic ’ For poorly sampled mosaics, ‘ft’ is better

54. CASA Tutorial – Santiago Jan. 26, 2009 54 More clean Mosaicing parameters continued: mosweight : important/different for uniform and Brigg's weighting scheme. Use per field weighting if mosweight=True Cotton-Scwab major cycles imagermode=’csclean’ or ‘mosaic’ returns to residual visibilities at major cycles cyclefactor : controls major cycle depth larger => more major cycles (clean will take longer) to a lesser extent cyclespeedup (for a non- converging clean)

55. CASA Tutorial – Santiago Jan. 26, 2009 55 Image Display The viewer Cookbook Chapter 7

56. CASA Tutorial – Santiago Jan. 26, 2009 56 Image Analysis see Chapter 6 of Cookbook task imhead - get and change image header information task immoments - computes moment images of spectral cube task immath - combine images and do image math using Lattice Expression Language (LEL) also: Spectral Index, Linear Polarized Intensity and Angle task imstat - return statistics on regions of image task imval - return values for pixel or region of image task imfit - fit a 2D Gaussian to the image

57. CASA Tutorial – Santiago Jan. 26, 2009 57 Task immoments use viewer to look at NGC5921 moment images Overlay contours of moment 1 (velocity) on moment 0 (intensity)

58. CASA Tutorial – Santiago Jan. 26, 2009 58 V - Scripts & Data Tutorial Home Page http://http://www.cv.nrao.edu/~cbrogan/2009126.htm CASA Scripts & Data Page http://casa.nrao.edu/casatraining.shtml

59. CASA Tutorial – Santiago Jan. 26, 2009 59 Crashes & Recovery Beta Release still has crash modes plotting in particular (plotxy and plotcal) can get a segmentation fault If in doubt, exit and restart casapy get rid of orphaned loggers you may have to use ps to find rogue casapy processes and kill them

60. CASA Tutorial – Santiago Jan. 26, 2009 60 Beta Disclaimer This really is a Beta Release! still missing functionality there are known failure modes Improvements in upcoming patches move towards handling ALMA/EVLA “use cases” better handling of calibration

61. CASA Tutorial – Santiago Jan. 26, 2009 Next Steps 61 Everyone run the fast VLA script ngc5921_demo.py to ensure things are working properly Then you can run through the extensively annotated script for reduction of BIMA SONG data: ngc4926_tutorial.py Or for the VERY brave and patient…

62. CASA Tutorial – Santiago Jan. 26, 2009 New ‘Beta’ SMA Data Reduction Script Available 62 http:www.cv.nrao.edu/~cbrogan/sma_reduction Many of the slow aspects of running this script: plotting, flagging, scratch column creation are actively being worked on this cycle – patience is required CARMA reduction is similarly possible via miriad: uvfits (be sure to do linelength correction first) to casapy: importuvfits. The NAASC has formed a collaboration with the U. of Maryland to write a “CARMA filler” – hopefully finished by end of summer

63. CASA Tutorial – Santiago Jan. 26, 2009 63