M100 Band3 SingleDish 4.5

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DO NOT USE IT. For the release CASA version (4.3), please go go M100_Band3_SingleDish_4.3

To navigate the CASAguides pages, visit [1]

  • This guide requires CASA 4.5 and assumes that you have downloaded M100_Band3_TP_UncalibratedData.tgz as described in M100_Band3#Obtaining_the_Data
  • Details of the ALMA observations are described at M100_Band3
  • This portion of the guide covers calibration and imaging starting from the raw visibility data.

Overview

This portion of CASA Guide will cover the data reduction of the Total Power (TP) array observations of M100. The data consist of "amplitude calibrator" datasets (containing observational data of the quasar 3C279) and "science" datasets containing data for the science target M100. The data are reduced in the following steps:

  • Science datasets are calibrated into units of Kelvins ('Antenna' temperature units - i.e. not scaled for main beam efficiency).
  • Amplitude Calibrator observations of 3c279 are calibrated also into Antenna temperature units, and an image of the calibrator, for each observation session, is generated.
  • The radio continuum emission from 3C279 in the amplitude calibrator data are used to derive the Jansky/Kelvin (Jy/K) factors for individual days and frequencies (spectral windows) and are applied to the science data to convert the science data into Jy/beam units.
  • The calibrated science data are imaged into a data cube.

The combination of the resultant image with the interferometric (12-m array and 7-m array) data is explained in a separate page, valid for both CASA versions 4.3 and 4.5 M100_Band3_Combine_4.3.

This guide is designed for CASA 4.5.0.


Confirm Your Version of CASA

This guide has been written for CASA release 4.5.0.,Please confirm your version before proceeding. The value returned from casadef.casa_version should be 4.5.0. If not, please obtain at least version 4.5.0 (or later), from [2]

# In CASA
casadef.casa_version
Out[2]: '4.5.0'

Summary of Datasets

The observations were made on the 1st, 5th, 7th, and 17th July 2014, using two or three 12-m antennas and the ACA correlator. The table below indicates the ID's of the Execution Blocks, their start and end times, and the antennas in the array. There are nine science datasets (i.e., two or three per day).

#Science
uid___A002_X85c183_X36f      Observed from 2014-07-01T21:51:26.2 to 2014-07-01T22:40:28.4 (UTC)      DA61, PM03, PM04
uid___A002_X85c183_X60b      Observed from 2014-07-01T22:43:50.0 to 2014-07-01T23:32:39.6 (UTC)      DA61, PM03, PM04
uid___A002_X8602fa_X2ab      Observed from 2014-07-05T23:58:03.6 to 2014-07-06T00:46:52.0 (UTC)      PM02, PM03, PM04
uid___A002_X8602fa_X577      Observed from 2014-07-06T00:55:17.8 to 2014-07-06T01:44:07.3 (UTC)      PM02, PM03, PM04
uid___A002_X864236_X2d4      Observed from 2014-07-07T23:03:48.1 to 2014-07-07T23:53:47.9 (UTC)      PM03, PM04
uid___A002_X864236_X693      Observed from 2014-07-07T23:56:09.6 to 2014-07-08T00:46:07.1 (UTC)      PM03, PM04
uid___A002_X86fcfa_Xd9       Observed from 2014-07-17T20:55:15.5 to 2014-07-17T21:44:06.1 (UTC)      DV10, PM03, PM04
uid___A002_X86fcfa_X664      Observed from 2014-07-17T22:24:17.3 to 2014-07-17T23:13:08.0 (UTC)      DV10, PM03, PM04
uid___A002_X86fcfa_X96c      Observed from 2014-07-17T23:23:37.0 to 2014-07-18T00:12:25.3 (UTC)      DV10, PM03, PM04

Similarly, the concomitant Calibration datasets (used to convert from Antenna temperature units into Jy/beam units, for combination), are:

#Amplitude Calibrator
uid___A002_X85c183_X895      Observed from 2014-07-01T23:35:23.1 to 2014-07-02T00:07:54.6 (UTC)      DA61, PM03, PM04
uid___A002_X8602fa_Xc3       Observed from 2014-07-05T23:21:25.6 to 2014-07-05T23:53:41.0 (UTC)      PM02, PM03, PM04
uid___A002_X864236_Xe1       Observed from 2014-07-07T22:27:35.4 to 2014-07-07T23:01:05.7 (UTC)      PM03, PM04
uid___A002_X86fcfa_X3ae      Observed from 2014-07-17T21:48:30.0 to 2014-07-17T22:20:52.2 (UTC)      DV10, PM03, PM04

Script Calibration

In this Guide, the data are calibrated into Antenna temperature in units of K. This is done in the steps that are described in the steps under Manual calibration, using only one of the science sets as an example: uid___A002_X85c183_X36f, However, there are another eight datafiles to be processed. If you wish to automatically and non-interactively calibrate all the science data without working through the steps, you can instead execute the script M100.casa4p5.calib.py using the execfile command.

# In CASA
execfile('M100.casa4p5.calib.py')

Manual Calibration

There are three basic steps to the Calibration of the Science data:

  1. Import, inspection and flagging
  2. Calibration
    • Sky and bandpass calibration (i.e. Tsys and frequency sampling function)
    • Adjustment for Correlator non-linearity
    • Conversion to Jy/beam
  3. Imaging

Import, inspection and flagging

Import

The first thing to do is to convert the dataset into the CASA Measurement Set (MS) format. The raw data have been provided to you in the ASDM (ALMA Science Data Model), which is the native format of the data produced by the observatory but cannot be processed by CASA. The conversion from ASDM to MS is done with the task importasdm.

# In CASA
importasdm('uid___A002_X85c183_X36f',
           asis='Antenna Station Receiver Source CalAtmosphere CalWVR',
           bdfflags=True)

The converted dataset (with a suffix ".ms") is created with data flags embedded in the binary files in the ASDM dataset (so-called "BDF flags") necessary for single-dish data.

Inspection - listobs

After import,the usual first step is then to get some basic information about the data. We do this using the task listobs, which will output a detailed summary of each dataset supplied.

# In CASA
listobs(vis='uid___A002_X85c183_X36f.ms',
        listfile='uid___A002_X85c183_X36f.ms.listobs')

The output will be sent to the CASA logger, and also written in a file named uid___A002_X85c183_X36f.ms.listobs which you can view at your leisure. listobs displays information about the targets, dates, frequencies, etc. Below is an excerpt from listobs for uid___A002_X85c183_X36f:

Fields: 2
  ID   Code Name                RA               Decl           Epoch   SrcId      nRows
  0    none J1215+1654          12:15:03.979140 +16.54.37.95680 J2000   0          14661
  1    none M100                12:22:54.360000 +15.48.50.60000 J2000   1          61653
Spectral Windows:  (25 unique spectral windows and 2 unique polarization setups)
  SpwID  Name                           #Chans   Frame   Ch0(MHz)  ChanWid(kHz)  TotBW(kHz) CtrFreq(MHz) BBC Num  Corrs  
  0      WVR#NOMINAL                         4   TOPO  184550.000   1500000.000   7500000.0 187550.0000        0  XX
  1      ALMA_RB_03#BB_1#SW-01#FULL_RES    124   TOPO   91955.512    -15625.000   1937500.0  90994.5750        1  XX  YY
  2      ALMA_RB_03#BB_1#SW-01#CH_AVG        1   TOPO   90978.950   1734375.000   1734375.0  90978.9500        1  XX  YY
  3      ALMA_RB_03#BB_2#SW-01#FULL_RES    124   TOPO   93893.012    -15625.000   1937500.0  92932.0750        2  XX  YY
  4      ALMA_RB_03#BB_2#SW-01#CH_AVG        1   TOPO   92924.262   1937500.000   1937500.0  92924.2625        2  XX  YY
  5      ALMA_RB_03#BB_3#SW-01#FULL_RES    124   TOPO  102033.637     15625.000   1937500.0 102994.5750        3  XX  YY
  6      ALMA_RB_03#BB_3#SW-01#CH_AVG        1   TOPO  102986.762   1937500.000   1937500.0 102986.7625        3  XX  YY
  7      ALMA_RB_03#BB_4#SW-01#FULL_RES    124   TOPO  104033.637     15625.000   1937500.0 104994.5750        4  XX  YY
  8      ALMA_RB_03#BB_4#SW-01#CH_AVG        1   TOPO  104986.762   1937500.000   1937500.0 104986.7625        4  XX  YY
  9      ALMA_RB_03#BB_1#SW-01#FULL_RES    128   TOPO  101942.187    -15625.000   2000000.0 100950.0000        1  XX  YY
  10     ALMA_RB_03#BB_1#SW-01#CH_AVG        1   TOPO  100926.562   1781250.000   1781250.0 100926.5625        1  XX  YY
  11     ALMA_RB_03#BB_2#SW-01#FULL_RES    128   TOPO  103757.337    -15625.000   2000000.0 102765.1500        2  XX  YY
  12     ALMA_RB_03#BB_2#SW-01#CH_AVG        1   TOPO  102741.712   1781250.000   1781250.0 102741.7125        2  XX  YY
  13     ALMA_RB_03#BB_3#SW-01#FULL_RES    128   TOPO  111814.962     15625.000   2000000.0 112807.1500        3  XX  YY
  14     ALMA_RB_03#BB_3#SW-01#CH_AVG        1   TOPO  112783.712   1781250.000   1781250.0 112783.7125        3  XX  YY
  15     ALMA_RB_03#BB_4#SW-01#FULL_RES    128   TOPO  113689.962     15625.000   2000000.0 114682.1500        4  XX  YY
  16     ALMA_RB_03#BB_4#SW-01#CH_AVG        1   TOPO  114658.712   1781250.000   1781250.0 114658.7125        4  XX  YY
  17     ALMA_RB_03#BB_1#SW-01#FULL_RES   4080   TOPO  101945.850      -488.281   1992187.5 100950.0000        1  XX  YY
  18     ALMA_RB_03#BB_1#SW-01#CH_AVG        1   TOPO  100949.756   1992187.500   1992187.5 100949.7559        1  XX  YY
  19     ALMA_RB_03#BB_2#SW-01#FULL_RES   4080   TOPO  103761.000      -488.281   1992187.5 102765.1500        2  XX  YY
  20     ALMA_RB_03#BB_2#SW-01#CH_AVG        1   TOPO  102764.906   1992187.500   1992187.5 102764.9059        2  XX  YY
  21     ALMA_RB_03#BB_3#SW-01#FULL_RES   4080   TOPO  111811.300       488.281   1992187.5 112807.1500        3  XX  YY
  22     ALMA_RB_03#BB_3#SW-01#CH_AVG        1   TOPO  112806.906   1992187.500   1992187.5 112806.9059        3  XX  YY
  23     ALMA_RB_03#BB_4#SW-01#FULL_RES   4080   TOPO  113686.300       488.281   1992187.5 114682.1500        4  XX  YY
  24     ALMA_RB_03#BB_4#SW-01#CH_AVG        1   TOPO  114681.906   1992187.500   1992187.5 114681.9059        4  XX  YY
Sources: 48
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
  0    J1215+1654          0     -              -            
  0    J1215+1654          25    -              -            
  0    J1215+1654          26    -              -            
  0    J1215+1654          27    -              -            
  0    J1215+1654          1     -              -            
  0    J1215+1654          2     -              -            
  0    J1215+1654          3     -              -            
  0    J1215+1654          4     -              -            
  0    J1215+1654          5     -              -            
  0    J1215+1654          6     -              -            
  0    J1215+1654          7     -              -            
  0    J1215+1654          8     -              -            
  0    J1215+1654          9     -              -            
  0    J1215+1654          10    -              -            
  0    J1215+1654          11    -              -            
  0    J1215+1654          12    -              -            
  0    J1215+1654          13    -              -            
  0    J1215+1654          14    -              -            
  0    J1215+1654          15    -              -            
  0    J1215+1654          16    -              -            
  0    J1215+1654          17    100950         0            
  0    J1215+1654          18    100950         0            
  0    J1215+1654          19    102794.1       0            
  0    J1215+1654          20    102794.1       0            
  0    J1215+1654          21    112794.1       0            
  0    J1215+1654          22    112794.1       0            
  0    J1215+1654          23    114669.1       0            
  0    J1215+1654          24    114669.1       0            
  1    M100                0     -              -            
  1    M100                25    -              -            
  1    M100                26    -              -            
  1    M100                27    -              -            
  1    M100                9     -              -            
  1    M100                10    -              -            
  1    M100                11    -              -            
  1    M100                12    -              -            
  1    M100                13    -              -            
  1    M100                14    -              -            
  1    M100                15    -              -            
  1    M100                16    -              -            
  1    M100                17    100950         0            
  1    M100                18    100950         0            
  1    M100                19    102794.1       0            
  1    M100                20    102794.1       0            
  1    M100                21    112794.1       0            
  1    M100                22    112794.1       0            
  1    M100                23    114669.1       0            
  1    M100                24    114669.1       0            
Antennas: 3:
  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
                                                                     East         North     Elevation               x               y               z
  0    DA61  A075      12.0 m   -067.45.17.9  -22.53.21.4         -4.5609     -499.7012       23.0322  2225072.419944 -5440148.858968 -2481499.171703
  1    PM03  T701      12.0 m   -067.45.18.8  -22.53.22.2        -29.1265     -522.7875       22.2052  2225045.995589 -5440149.141967 -2481520.118569
  2    PM04  T703      12.0 m   -067.45.16.2  -22.53.23.9         42.8797     -575.6910       21.7763  2225104.700870 -5440102.471978 -2481568.689518

From this output you can for example see the followings.

  • From "Data records" section (not shown here): The execution consists of 15 scans with various scan intents.
    • Scans 1 and 2 are pointing and sideband gain ratio calibrations (done interferometrically), which need to be done prior to observing the target, on the quasar J1215+1654.
    • Scans 3 and 4 are interferometric delay and system noise temperature (Tsys) measurements also on J1215+1654 (they are in principle unnecessary; just a hack to make things happen on the telescope control software).
    • Scans 6, 7, 9, 10, 12, 13, and 15, whose scan intents contain "OBSERVE_TARGET", are for raster mapping of the target M100. The associated spectral window (SPW) ID's are 0 and 17-24.
    • Scans 5, 8, 11, and 14 with scan intents "CALIBRATE_ATMOSPHERE" are Tsys measurements for M100. The SPW ID's for Tsys scans are 0 and 9-16.
  • From "Spectral Windows" section:
    • SPW 0 contains the Water Vapor Radiometer (WVR) data, which are taken for all scans, but which are not used here.
    • SPW's 1, 3, 5, and 7 are placed on standard continuum frequencies and are used for the pointing scan only.
    • SPW's 9, 11, 13, and 15 cover the same frequency range as the science SPW's (see the next bullet) and are used to measure the Tsys used for calibration. They have 128 spectral channels (15.6 MHz spacing) in 2000 MHz bandwidth.
    • SPW's 17, 19, 21, and 23 cover the frequency ranges used for the actual science observations. They have 4080 spectral channels (488 kHz spacing) in 1992 MHz bandwidth. Hereafter these SPW's are referred to as "science" SPW's. The target line, CO J=1-0, is placed in SPW 23, the corresponding Tsys is taken from SPW 15.
    • The remaining, even-number SPW's contain channel-averages of the actually used SPW's (e.g., SPW 24 corresponds to SPW 23 averaged into one channel).
  • From "Antennas" section: Three 12-m antennas (DA61, PM03, and PM04) were used for the observations.

Inspection - scanpattern

The scan pattern of the raster mapping can be visualized by issueing the following command. A plot will be shown in a window and also saved as a PNG file uid___A002_X85c183_X36f.ms.sampling.png.

Figure 1: The scan pattern of the raster mapping for uid___A002_X85c183_X36f.
# In CASA
aU.getTPSampling(vis='uid___A002_X85c183_X36f.ms',
                 showplot=True,
                 plotfile='uid___A002_X85c183_X36f.ms.sampling.png')

Inspection - System Noise Temperature

Let's start by checking the Tsys. We use the task gencal to extract the Tsys into a CASA calibration table. This table is only used for inspection of Tsys quality, and not in further processing.

# In CASA
gencal(vis='uid___A002_X85c183_X36f.ms',
       caltable='uid___A002_X85c183_X36f.ms.tsys',
       caltype='tsys')

The generated Tsys calibration table can be plotted using the task Template:Plot bandpass. The generated plots are saved in the directories uid___A002_X85c183_X36f.ms.tsys.plots.overlayTime and uid___A002_X85c183_X36f.ms.tsys.plots.

Figure 2: The Tsys as a function of frequency for DA61 in uid___A002_X85c183_X36f. Colors represent time.
Figure 3: The Tsys as a function of frequency for SPW 15 in uid___A002_X85c183_X36f. Colors represent antennas.
# In CASA
plotbandpass(caltable='uid___A002_X85c183_X36f.ms.tsys',
             overlay='time',
             xaxis='freq',
             yaxis='amp',
             subplot=22,
             buildpdf=False,
             interactive=False,
             showatm=True,
             pwv='auto',
             chanrange='5~123',
             showfdm=True,
             field='',
             figfile='uid___A002_X85c183_X36f.ms.tsys.plots.overlayTime/uid___A002_X85c183_X36f.ms.tsys')

Flagging

Although the "science" SPW's have 1992 MHz bandwidths with 4080 spectral channels, their edge channels are very noisy, because each intermediate frequency signal path (baseband) is equipped with a bandpass filter of ~1.8 GHz width. Note that this is not necessarily always the case, however unless a spectral line of interest falls at the edges of the spectral windows, it is in general, safest to flag out the edge channels. We flag 120 channels on each side of the "science" SPW's. As a result 3840 channels (1875 MHz bandwidth), i.e., the same number of channels and bandwidth as FDM SPW's in the 12-m array data, remain in each SPW.

# In CASA
flagdata(vis = 'uid___A002_X85c183_X36f.ms',
       mode = 'manual',
       spw = '17:0~119;3960~4079,19:0~119;3960~4079,21:0~119;3960~4079,23:0~119;3960~4079',
       action = 'apply',
       flagbackup = True)

Tsys Calibration

We calibrate the data into Antenna temperature in units of K, using the equation Ta* = Tsys*(ON-OFF)/OFF, where ON and OFF are the data on-source (i.e., during the raster scanning) and off-source (on a reference position where only background emission exists), respectively. The calibration is done by the task tsdcal which requires matching of list of the "science" and Tsys spectral windows. Tsys observations will always have 128 channels over 2GHz bandwidth, and as described in listobs, we already know which spectral windows match the science spectral windows most closely, in frequency. for example, spectral window 9, with 128 channels matches well with spectral window 17, 11 with 19, 13 with 21 and 15 with 2. Thus, we form the Tsys and Science spectral window mapping input parameters, with the syntax: {9:[17], 11:[19], 13:[21],15:[23]}

  9      ALMA_RB_03#BB_1#SW-01#FULL_RES    128   TOPO  101942.187    -15625.000   2000000.0 100950.0000        1  XX  YY
  .
  .
  17     ALMA_RB_03#BB_1#SW-01#FULL_RES   4080   TOPO  101945.850      -488.281   1992187.5 100950.0000        1  XX  YY
  11     ALMA_RB_03#BB_2#SW-01#FULL_RES    128   TOPO  103757.337    -15625.000   2000000.0 102765.1500        2  XX  YY
  .
  .
  19     ALMA_RB_03#BB_2#SW-01#FULL_RES   4080   TOPO  103761.000      -488.281   1992187.5 102765.1500        2  XX  YY
  13     ALMA_RB_03#BB_3#SW-01#FULL_RES    128   TOPO  111814.962     15625.000   2000000.0 112807.1500        3  XX  YY
  .
  .
  21     ALMA_RB_03#BB_3#SW-01#FULL_RES   4080   TOPO  111811.300       488.281   1992187.5 112807.1500        3  XX  YY
  15     ALMA_RB_03#BB_4#SW-01#FULL_RES    128   TOPO  113689.962     15625.000   2000000.0 114682.1500        4  XX  YY
  .
  .
  23     ALMA_RB_03#BB_4#SW-01#FULL_RES   4080   TOPO  113686.300       488.281   1992187.5 114682.1500        4  XX  YY

And the Tsys calibration command is formed like the following:

# In CASA
tsdcal(infile = 'uid___A002_X85c183_X36f.ms',
    calmode = 'ps,tsys,apply',
    spwmap = {9:[17], 11:[19], 13:[21],15:[23]},
    spw = '9,11,13,15,17,19,21,23')

Note: that in this step, the calibrations are applied in situ. That is: the calibrated data are written into the original data - however it is written in such a way that any additional calls to tsdcal will not apply any further calibrations. We will examine the quality of the bandpass and Tsys calibration after the correction for non-linearity, next.

The calibrated bandpasses, averaged over each scan, can be plotted with:

# In CASA
plotms(vis='uid___A002_X85c183_X36f.ms',
    xaxis='freq', yaxis='amp', ydatacolumn='corrected',
    field='M100',spw='23',
    scan='6,7,9,10,12,13,15',
    averagedata=T,avgtime='9999',
    gridcols=3,gridrows=3,iteraxis='scan',
    plotrange=[113.5, 116, -0.01, 0.08],
    plotfile='vis.png',
    showgui=F)

Note: For amplitude calibrator datasets, (as opposed to science target maps) the calmode option for tsdcal should be 'otfraster,tsys,apply' ('otfraster' instead of 'ps'). 'otfraster' tells the task to use both ends of each raster row as "OFF" data (as opposed to a dedicated "OFF" sky measurement). This is because temporal fluctuation of atmospheric emission is the dominant source of noise in radio continuum observations, and hence the "OFF" needs to be as close as possible to the "ON" in time (and spatial location).

Application of Non-Linearity Correction Factor

In Cycle 1 and 2, single-dish data taken with the ACA correlator suffer from non-linearity which originates in the digital signal processing. Its impact was thoroughly studied both experimentally and theoretically, and it was concluded that multiplication by a correction factor of 1.25 yields an amplitude accuracy of +/-5%.

To preserve the data history, we use here the tasks split to split out the science corrected data columns - note that from here on, the spectral windows are renumbered: [0,1,2,3]. We then generate a calibration table, using a defined function to_amp_factor, with gencal. Finally, we apply the calibration with applycal We apply the correction here using tasks genial and applycal - this is different to the methods used in the past, and are available now because of the migration to MS-only format of Single-dish CASA.

Note: The ACA online software has been equipped with this correction for data later than cycle 3. Thus this step is unnecessary for data taken later than cycle 2.

# In CASA
to_amp_factor = lambda x: 1. / sqrt(x)

split(vis='uid___A002_X85c183_X36f.ms',
    outputvis='uid___A002_X85c183_X36f.ms.cal.split',
    datacolumn='corrected',
    spw='17,19,21,23')

gencal(vis='uid___A002_X85c183_X36f.ms.cal.split',
    caltable='uid___A002_X85c183_X36f.ms.nlc',
    caltype='amp', spw='',
    parameter=map(to_amp_factor, [1.25]))

applycal(vis='uid___A002_X85c183_X36f.ms.cal.split',
    gaintable='uid___A002_X85c183_X36f.ms.nlc')

Baseline Subtraction (only for Science Datasets)

Note: this step is appropriate for spectral line observations (science datasets) but should not be done for the continuum observations (amplitude calibrator datasets) -- it would eliminate the continuum emission!

We will subtract low-order spectral baselines using the task tsdbaseline. Typically these manifest from structure in the distribution of water in the atmosphere: the ON and OFF positions are slightly different, and the difference manifests as - typically - a low frequency variation in the spectra. The situation is exacerbated for observations closer to water lines and also for higher frequencies.

# In CASA
tsdbaseline(infile='uid___A002_X85c183_X36f.ms.cal.split',
    datacolumn='corrected',
     spw='',
     blfunc='poly',
     order=1,
     outfile='uid___A002_X85c183_X36f.ms.bl',
     overwrite=True)

The spectra can be checked using plotms, which we have already used in a previous step.

# In CASA
plotms(vis='uid___A002_X85c183_X36f.ms.bl',
    xaxis='freq', yaxis='amp', ydatacolumn='corrected',
    field='M100',spw='3',
    scan='6,7,9,10,12,13,15',
    averagedata=T,avgtime='9999',
    gridcols=3,gridrows=3,iteraxis='scan',
    plotrange=[113.5, 116, -0.01, 0.08],
    plotfile='vis_bl.png',
    showgui=F)

or also with sdplot:

Figure 4: The spectra after baseline subtraction for DA61 SPW 23 in uid___A002_X85c183_X36f. Colors represent polarizations.
# In CASA
sdplot(infile='uid___A002_X85c183_X36f.ms.bl',
    antenna='PM03',
    fluxunit='amp',
    specunit='GHz',
    field='M100',
    spw='3',
    scan='6,7,9,10,12,13,15',
    rastermode='row',
    timeaverage=T,
    scanaverage=T,
    plottype='spectra',
    stack='p',
    panel='s',
    flrange=[-0.1,0.16],
    sprange=[113.5,116],
    subplot=33
    outfile='vis_bl_plotms.png')

We do not concatenate separate Execution Blocks, because we need to determine and apply day-by-day Jy/K conversion factor.

Note that one of the antennas, PM02, had a problem in the first baseband (SPW 17) on 2014-07-05, and its impact may not be specific to this one SPW (e.g., it may have resulted in poor pointing calibration). Therefore the PM02 data should be flagged from the affected datasets: uid___A002_X8602fa_X2ab (science), and uid___A002_X8602fa_X577 (science). The calibrator set uid___A002_X8602fa_Xc3 will also be affected, and will be flagged out in the subsequent processing of the calibrators.

# In CASA
flagdata(vis='uid___A002_X8602fa_X2ab.ms.bl',
    antenna='PM02')
flagdata(vis='uid___A002_X8602fa_X577.ms.bl',
    antenna='PM02')


Convert the Science Target Units from Kelvin to Jansky

At this stage the data have been calibrated into units of antenna temperature, in Kelvins.

It now remains to convert the science data into Jy/beam units - the Jy per K factors. This is important for combination of the data, with 7m and 12m sets. Later in this guide we show how to determine the correct factors from the calibrator datasets, for conversion (the process is essentially identical to processing the science datasets, with the exception that the baseline step is omitted from the calibration dataset processing). However to determine the factors, the calibration data must also be imaged and then interrogated to determine the appropriate values. This is the last step in the script M100.casa4p5.calib.py.

As before, we refer only to one ASDM: uid___A002_X85c183_X36f. The script should be consulted for treatment of all the M100 Single-dish ASDMs (and the correct application of the Jy per K factors). Again, we apply the factors by making use of the gencal and applycal tasks. Also as before, we make use of the python function defined earlier: to_amp_factor


# In CASA

factors = [41.37, 42.39, 43.45, 42.82]
gencal(vis='uid___A002_X85c183_X36f.ms.bl',
    caltable=jypkcaltable,
    caltype='amp',
    spw='0,1,2,3',
    parameter=map(to_amp_factor, jyperk))

applycal(vis='uid___A002_X85c183_X36f.ms.bl',
    gaintable=jypkcaltable)

Image the Science Target

With the science datasets have been calibrated into Jy/beam units, the final step is to image the science data. This step is done by the script "ScriptForImagingScienceTarget.py" (run execfile('ScriptForImagingScienceTarget.py') in CASA).

Define the list of the calibrated science datasets, which the CASA task sdimaging accepts.

# In CASA
sciencedata = [('%s.ms.cal.jy' % name) for name in basename_science]

Obtain the data sampling and determine the cell spacing and map size based on the mean frequency of the target SPW. This part is in principle the same as the corresponding procedure in the "Optionally Image the Amplitude Calibrator and Measure the Value of Jy/K" section. Please refer to the script "ScriptForImagingAmpCalAndDerivingJyPerK.py" used there.

# In CASA
fwhmfactor = 1.13
diameter = 12

xSampling, ySampling, maxsize = aU.getTPSampling(sciencedata[0], showplot=False)

spw = 23

msmd.open(sciencedata[0])
freq = msmd.meanfreq(spw)
msmd.close()
print "SPW %d: %.3f GHz" % (spw, freq*1e-9)

theorybeam = aU.primaryBeamArcsec(frequency=freq*1e-9,
                                  fwhmfactor=fwhmfactor,
                                  diameter=diameter)

cell = theorybeam/9.0
imsize = int(round(maxsize/cell)*2)

Now the data are imaged. The velocity channel maps of the CO J=1-0 line (restfreq='115.271201800GHz') are created as a data cube which covers the velocity range of 1400-1700 km/s at a spacing of 5 km/s (start='1400km/s', width='5km/s', nchan=70).

Note: The Jy/K value depends on the parameters of gridding convolution (i.e., "gridfunction", "cell", and function-specific parameters ["convsupport" for gridfunction='SF']). That is, the same gridding parameters should be used for both amplitude calibrator and science images -- otherwise the calibration into Jy unit becomes invalid.

# In CASA
sdimaging(infiles=sciencedata,
          field='M100',
          spw='%d' % spw,  #sciencespw
          nchan=70,
          mode='velocity',
          start='1400km/s',
          width='5km/s',
          veltype='radio',
          outframe='lsrk',
          restfreq='115.271201800GHz',
          gridfunction='SF',
          convsupport=6,
          stokes='',
          phasecenter='J2000 12h22m54.9 +15d49m15',
          ephemsrcname='',
          imsize=imsize,
          cell=str(cell)+'arcsec',
          overwrite=True,
          outfile='M100_TP_CO_cube.image')

The produced image has the brightness unit of K in the image header, which is not correct. Modify the header using the task imhead.

# In CASA
imhead(imagename='M100_TP_CO_cube.image',
       mode='put',
       hdkey='bunit',
       hdvalue='Jy/beam')

(Optionally) Subtract a Residual Background from the Image

Now you can browse the data cube using the viewer.

# In CASA
viewer('M100_TP_CO_cube.image')

If you plot the line profile using the viewer, you may notice that the background (i.e., line-free channels) level is slightly negative. To correct this, spectral baselines are subtracted from the image using the task imcontsub.

# In CASA
imcontsub(imagename='M100_TP_CO_cube.image',
          linefile='M100_TP_CO_cube.bl.image',
          contfile='M100.ignorethis.image',
          fitorder=1,
          chans='0~7;62~69')
os.system('rm -rf M100.ignorethis.image')

The main cause of the negative baseline is the following. The task sdbaseline with maskmode='auto' is supposed to find lines from the data and exclude the detected lines from baseline fitting. However, the CO line from M100 is not bright enough to be detected from individual spectra (1-s integration), and hence sdbaseline included the velocity ranges of the line into baseline fitting. The impact of this effect would be smaller if the line is brighter, or narrower w.r.t. the correlator bandwidth.

Add Restoring Beam Header Information to the Science Image

The image does not have the beam size, which is necessary for combining the image with interferometric data, in the header. The beam size (including the broadening due to gridding convolution and data sampling) is calculated using the function sfBeam of the Analysis Utilities and then written into the header using the functions of the ia tool.

# In CASA
minor, major, fwhmsfBeam, sfBeam = aU.sfBeam(frequency=freq*1e-9,
        pixelsize=cell,
        convsupport=6,
        img=None, #to use Gaussian theorybeam
        stokes='both',
        xSamplingArcsec=xSampling,
        ySamplingArcsec=ySampling,
        fwhmfactor=fwhmfactor,
        diameter=diameter)

ia.open('M100_TP_CO_cube.bl.image')
ia.setrestoringbeam(major=str(sfBeam)+'arcsec', minor=str(sfBeam)+'arcsec', pa='0deg')
ia.done()

Quick Look at the Results

Make a 0th moment (integrated intensity) map using the task immoments and browse it using the viewer.

Figure 5: The integrated intensity map of M100.
# In CASA
os.system('rm -rf *M100_TP_CO_cube.bl.image.mom0')
immoments(imagename='M100_TP_CO_cube.bl.image',
          moments=[0],
          axis='spectral',
          chans='8~61',
          outfile='M100_TP_CO_cube.bl.image.mom0')

viewer('M100_TP_CO_cube.bl.image.mom0')

Import "Analysis Utilities"

The Analysis_Utilities package will be used for the following processes. Import the package and instantiate the stuffForScienceDataReduction class therein.

# In CASA
import analysisUtils as aU
es = aU.stuffForScienceDataReduction()

Optionally Image the Amplitude Calibrator and Measure the Value of Jy/K

Determination of the Jy/K conversion factor is achieved by imaging a source whose continuum flux is known and measuring the observed brightness temperature. One observation of this source - the amplitude calibrator - was made per day, giving a total of four datasets (see top).

The true size of the beam (point spread function), on which the Jy/K value depends, in a map is determined be several ingredients.

  • The intrinsic beam size is determined by the antenna diameter and optics (and of course wavelength). Here we assume the intrinsic beam size of 1.13*lambda/D, where D=12 [m] is the diameter of the antennas, and the factor 1.13 is derived from the optics design of the ALMA 12-m antennas.
  • The effective beam size is broadened by the following causes:
    • The scanning pattern used to observe the map (i.e., sample spacing in both directions).
    • The method used to grid the individual spectra into a map/cube.

The Analysis Utilities provides several tools to get estimates of these.

If you wish to try this out for yourself, you will first need to download the raw amplitude calibrator data file M100_Band3_TP_ampcal_UncalibratedData.tgz. How to obtain the data is described at M100_Band3#Obtaining the Data. Once you have unpacked the data you will have a directory called M100_Band3_TP_ampcal_UncalibratedData. In this directory, execute the scripts for individual datasets (A002_X85c183_X895.ms.scriptForSDCalibration.py, A002_X8602fa_Xc3.ms.scriptForSDCalibration.py, A002_X864236_Xe1.ms.scriptForSDCalibration.py, and A002_X86fcfa_X3ae.ms.scriptForSDCalibration.py) to calibrate all four calibrator datasets (e.g., execfile('A002_X85c183_X895.ms.scriptForSDCalibration.py') in CASA). Then, run the script "ScriptForImagingAmpCalAndDerivingJyPerK.py", which uses for-loops to image the amplitude calibrator and calculate the Jy/K values (run execfile('ScriptForImagingAmpCalAndDerivingJyPerK.py') in CASA).

The resulting Jy/K values are as follows. Note that the values for individual antennas are averaged for each day, each SPW, because the antennas used for the Science observations were not necessarily available for the corresponding amplitude calibrator observations.

#Date        Amp_Cal_Dataset           SPW17   SPW19   SPW21   SPW23
2014-07-01   uid___A002_X85c183_X895   41.37   42.39   43.45   42.82
2014-07-05   uid___A002_X8602fa_Xc3    40.99   42.74   40.08   42.09
2014-07-07   uid___A002_X864236_Xe1    39.42   42.08   40.18   40.82
2014-07-17   uid___A002_X86fcfa_X3ae   43.49   43.70   42.01   43.04

Combination with 12m and 7m Array Data

If you wish to learn how to combine the Total Power data with interferometric 12m and 7m data, see the guide for Data Combination M100_Band3_Combine_4.3

Last checked on CASA Version 4.5.0.