NGC 5921: red-shifted HI emission 5.7.2
Overview
The technique used to calibrate and image continuum datasets generally applies to spectral line observations, except that an additional calibration step is required. Bandpass calibration flattens the spectral response of the observations, ensuring that spectral channel images are properly calibrated in amplitude and phase.
The following tutorial derives from an annotated script provided in the CASA Cookbook. The script is largely reproduced in sections and additionally annotated with figures and illustrations.
The data are included with the CASA installation.
Setting up the CASA Environment
Start up CASA in the directory you want to use.
# in bash
mkdir NGC5921
cd NGC5921
casapy
Now, in CASA, set up paths and global variables to facilitate the data reduction. These operations can be performed on-the-fly if you are reducing data interactively, but it's better to get them out of the way in the scripting environment.
import os
scriptmode = True
prefix = 'ngc5921.demo' # The prefix to use for all output files
# Set up some useful variables (these will be altered later on)
msfile = prefix + '.ms'
btable = prefix + '.bcal'
gtable = prefix + '.gcal'
ftable = prefix + '.fluxscale'
splitms = prefix + '.src.split.ms'
imname = prefix + '.cleanimg'
We'll use a python os command to get the appropriate CASA path for your installation. The use of os.environ.get is explained in the Appendix.
pathname=os.environ.get('CASAPATH').split()[0]
fitsdata=pathname+'/data/demo/NGC5921.fits'
Scripts are of course modified and repeated to the satisfaction of observer. To help clean up the bookkeeping and further avoid issues of write privileges, remove prior versions of the measurement set and calibration tables.
Tip: The first command in the following code block removes the measurement set. Depending on the size of the source data, refilling a measurement set can be time-consuming, and so you may want to consider editing a separate script that preserves the measurement set but skips the importuvfits command given below. This particular dataset is not very large and so refilling is fairly quick.
rmtables(msfile)
rmtables(btable)
rmtables(gtable)
rmtables(ftable)
rmtables(ftable)
rmtables(splitms+'*')
rmtables(imname+'.*')
rmtables(prefix+'.moments*')
# Final clean up of auxiliary files
os.system('rm -rf '+prefix+'*')
Import the Data
The next step is to import the multisource UVFITS data to a CASA measurement set via the importuvfits filler.
# Safest to start from task defaults
default('importuvfits')
# Set up the MS filename and save as new global variable
msfile = prefix + '.ms'
# Use task importuvfits
fitsfile = fitsdata
vis = msfile
saveinputs('importuvfits',prefix+'.importuvfits.saved')
importuvfits()
Saveinputs saves the parameters of a given command to specified text file, handy to debug a script and see what actually was run. Here, the parameters of importuvfits are saved to the file "ngc5921.demo.importuvfits.saved". Here's a listing of this file. Notice that it is executable with execfile in CASA (remove the # commenting symbol before importuvfits to have the execfile run the command).
CASA <71>: os.system('cat ngc5921.demo.importuvfits.saved')
taskname = "importuvfits"
fitsfile = "/usr/lib64/casapy/30.0.9709test-001/data/demo/NGC5921.fits"
vis = "ngc5921.demo.ms"
antnamescheme = "old"
#importuvfits(fitsfile="/usr/lib64/casapy/30.0.9709test-001/data/demo/NGC5921.fits",vis="ngc5921.demo.ms",antnamescheme="old")
A Summary of the Data
We'll need to have a look at the observing tables to learn the calibrator and source names. The relevant command is listobs.
listobs(vis='ngc5921.demo.ms', verbose=True)
The output goes to the logger window; see the screenshot at right.
Tip: You can control the text size of the logger window using <ctrl>-A (smaller font) and <ctrl>-L (larger font).
A more complete listing of the listobs output follows.
2009-12-03 16:15:38 INFO listobs ##### Begin Task: listobs ##### 2009-12-03 16:15:38 INFO listobs::::casa 2009-12-03 16:15:38 INFO listobs ================================================================================ 2009-12-03 16:15:38 INFO listobs MeasurementSet Name: /DATA/ASHLESHA_2/NGC5921/ngc5921.demo.ms MS Version 2 2009-12-03 16:15:38 INFO listobs ================================================================================ 2009-12-03 16:15:38 INFO listobs Observer: TEST Project: 2009-12-03 16:15:38 INFO listobs Observation: VLA 2009-12-03 16:15:38 INFO listobs Data records: 22653 Total integration time = 5280 seconds 2009-12-03 16:15:38 INFO listobs Observed from 13-Apr-1995/09:19:00.0 to 13-Apr-1995/10:47:00.0 (TAI) 2009-12-03 16:15:38 INFO listobs::ms::summary 2009-12-03 16:15:38 INFO listobs ObservationID = 0 ArrayID = 0 2009-12-03 16:15:38 INFO listobs Date Timerange (TAI) Scan FldId FieldName nVis Int(s) SpwIds 2009-12-03 16:15:38 INFO listobs 13-Apr-1995/09:19:00.0 - 09:24:30.0 1 0 1331+305000* 4509 30 [0] 2009-12-03 16:15:38 INFO listobs 09:27:30.0 - 09:29:30.0 2 1 1445+099000* 1890 30 [0] 2009-12-03 16:15:38 INFO listobs 09:33:00.0 - 09:48:00.0 3 2 N5921_2 6048 30 [0] 2009-12-03 16:15:38 INFO listobs 09:50:30.0 - 09:51:00.0 4 1 1445+099000* 756 30 [0] 2009-12-03 16:15:38 INFO listobs 10:22:00.0 - 10:23:00.0 5 1 1445+099000* 1134 30 [0] 2009-12-03 16:15:38 INFO listobs 10:26:00.0 - 10:43:00.0 6 2 N5921_2 6804 30 [0] 2009-12-03 16:15:38 INFO listobs 10:45:30.0 - 10:47:00.0 7 1 1445+099000* 1512 30 [0] 2009-12-03 16:15:38 INFO listobs (nVis = Total number of time/baseline visibilities per scan) 2009-12-03 16:15:38 INFO listobs Fields: 3 2009-12-03 16:15:38 INFO listobs ID Code Name RA Decl Epoch SrcId nVis 2009-12-03 16:15:38 INFO listobs 0 C 1331+305000* 13:31:08.2873 +30.30.32.9590 J2000 0 4509 2009-12-03 16:15:38 INFO listobs 1 A 1445+099000* 14:45:16.4656 +09.58.36.0730 J2000 1 5292 2009-12-03 16:15:38 INFO listobs 2 N5921_2 15:22:00.0000 +05.04.00.0000 J2000 2 12852 2009-12-03 16:15:38 INFO listobs (nVis = Total number of time/baseline visibilities per field) 2009-12-03 16:15:38 INFO listobs Spectral Windows: (1 unique spectral windows and 1 unique polarization setups) 2009-12-03 16:15:38 INFO listobs SpwID #Chans Frame Ch1(MHz) ChanWid(kHz)TotBW(kHz) Ref(MHz) Corrs 2009-12-03 16:15:38 INFO listobs 0 63 LSRK 1412.66507 24.4140625 1550.19688 1413.42801 RR LL 2009-12-03 16:15:38 INFO listobs Sources: 3 2009-12-03 16:15:38 INFO listobs ID Name SpwId RestFreq(MHz) SysVel(km/s) 2009-12-03 16:15:38 INFO listobs 0 1331+305000* 0 1420.405752 0 2009-12-03 16:15:38 INFO listobs 1 1445+099000* 0 1420.405752 0 2009-12-03 16:15:38 INFO listobs 2 N5921_2 0 1420.405752 0 2009-12-03 16:15:38 INFO listobs Antennas: 27: 2009-12-03 16:15:38 INFO listobs ID Name Station Diam. Long. Lat. 2009-12-03 16:15:38 INFO listobs 0 1 VLA:N7 25.0 m -107.37.07.2 +33.54.12.9 2009-12-03 16:15:38 INFO listobs 1 2 VLA:W1 25.0 m -107.37.05.9 +33.54.00.5 2009-12-03 16:15:38 INFO listobs 2 3 VLA:W2 25.0 m -107.37.07.4 +33.54.00.9 2009-12-03 16:15:38 INFO listobs 3 4 VLA:E1 25.0 m -107.37.05.7 +33.53.59.2 2009-12-03 16:15:38 INFO listobs 4 5 VLA:E3 25.0 m -107.37.02.8 +33.54.00.5 2009-12-03 16:15:38 INFO listobs 5 6 VLA:E9 25.0 m -107.36.45.1 +33.53.53.6 2009-12-03 16:15:38 INFO listobs 6 7 VLA:E6 25.0 m -107.36.55.6 +33.53.57.7 2009-12-03 16:15:38 INFO listobs 7 8 VLA:W8 25.0 m -107.37.21.6 +33.53.53.0 2009-12-03 16:15:38 INFO listobs 8 9 VLA:N5 25.0 m -107.37.06.7 +33.54.08.0 2009-12-03 16:15:38 INFO listobs 9 10 VLA:W3 25.0 m -107.37.08.9 +33.54.00.1 2009-12-03 16:15:38 INFO listobs 10 11 VLA:N4 25.0 m -107.37.06.5 +33.54.06.1 2009-12-03 16:15:38 INFO listobs 11 12 VLA:W5 25.0 m -107.37.13.0 +33.53.57.8 2009-12-03 16:15:38 INFO listobs 12 13 VLA:N3 25.0 m -107.37.06.3 +33.54.04.8 2009-12-03 16:15:38 INFO listobs 13 14 VLA:N1 25.0 m -107.37.06.0 +33.54.01.8 2009-12-03 16:15:38 INFO listobs 14 15 VLA:N2 25.0 m -107.37.06.2 +33.54.03.5 2009-12-03 16:15:38 INFO listobs 15 16 VLA:E7 25.0 m -107.36.52.4 +33.53.56.5 2009-12-03 16:15:38 INFO listobs 16 17 VLA:E8 25.0 m -107.36.48.9 +33.53.55.1 2009-12-03 16:15:38 INFO listobs 17 18 VLA:W4 25.0 m -107.37.10.8 +33.53.59.1 2009-12-03 16:15:38 INFO listobs 18 19 VLA:E5 25.0 m -107.36.58.4 +33.53.58.8 2009-12-03 16:15:38 INFO listobs 19 20 VLA:W9 25.0 m -107.37.25.1 +33.53.51.0 2009-12-03 16:15:38 INFO listobs 20 21 VLA:W6 25.0 m -107.37.15.6 +33.53.56.4 2009-12-03 16:15:38 INFO listobs 21 22 VLA:E4 25.0 m -107.37.00.8 +33.53.59.7 2009-12-03 16:15:38 INFO listobs 23 24 VLA:E2 25.0 m -107.37.04.4 +33.54.01.1 2009-12-03 16:15:38 INFO listobs 24 25 VLA:N6 25.0 m -107.37.06.9 +33.54.10.3 2009-12-03 16:15:38 INFO listobs 25 26 VLA:N9 25.0 m -107.37.07.8 +33.54.19.0 2009-12-03 16:15:38 INFO listobs 26 27 VLA:N8 25.0 m -107.37.07.5 +33.54.15.8 2009-12-03 16:15:38 INFO listobs 27 28 VLA:W7 25.0 m -107.37.18.4 +33.53.54.8 2009-12-03 16:15:38 INFO listobs::::casa 2009-12-03 16:15:38 INFO listobs ##### End Task: listobs ##### 2009-12-03 16:15:38 INFO listobs ##########################################
Appendix: Python Notes
os.environ.get
It's worth having a look at the output of the os.environ.get command to understand the python syntax. You can think of os.environ as a list of operating system environment variables, and get is a method that extracts information about the requested environment variable, here, CASAPATH. Get returns a string of whitespace separated information, and .split() turns that string into a list. The array index [0] extracts the first element of that list, which contains the path.
To illustrate, here is some example python I/O in CASA.
CASA <12>: print os.environ.get('CASAPATH')
/usr/lib64/casapy/30.0.9709test-001 linux local el5bld64b
CASA <13>: print os.environ.get('CASAPATH').split()
['/usr/lib64/casapy/30.0.9709test-001', 'linux', 'local', 'el5bld64b']
CASA <14>: print os.environ.get('CASAPATH').split()[0]
/usr/lib64/casapy/30.0.9709test-001
