View source for M100 Band3 SingleDish 4.2.2

M100 Single Dish Data Reduction (under modification by AH)


==Overview==

This portion of the '''[[M100 Band3 SingleDish 4.1]]''' CASA Guide will cover the reduction of the Total Power (TP) array data into units of Kelvins on the antenna temperature (Ta*) scale and imaging. 
Converting this image to the Jansky scale (Jy/beam) to be combined with interferometric data is covered in the '''[[M100 Band3 Combine 4.1]]''' section.

'''This guide is designed for CASA 4.1.0.

If you haven't downloaded the data, you can XXXXXXX and XXXXXX:

Once the download has finished, upack the file:

<source lang="bash">
# In a terminal outside CASA
tar -xvzf XXXsingledish_datasetXXX_TBD.tgz

cd XXrelevant_directoryXXX

# Start CASA
casapy
</source>

== Summary of Dataset ==

There were six observations made. The table below indicates the uid reference of each and the start and end times.

<pre style="background-color: #fffacd;">
uid___A002_X60b415_X39a     Observed from   14-Apr-2013/05:34:15.7   to   14-Apr-2013/05:58:23.8 (UTC)
uid___A002_X60b415_X6f7     Observed from   14-Apr-2013/06:23:03.0   to   14-Apr-2013/06:47:11.0 (UTC)
uid___A002_X6218fb_X264     Observed from   28-Apr-2013/04:12:06.1   to   28-Apr-2013/04:36:07.5 (UTC)
uid___A002_X6218fb_X425     Observed from   28-Apr-2013/04:38:56.8   to   28-Apr-2013/05:03:00.3 (UTC)
uid___A002_X6321c5_X3a7     Observed from   12-May-2013/02:22:16.9   to   12-May-2013/02:43:59.8 (UTC)
uid___A002_X6321c5_X5ca     Observed from   12-May-2013/02:47:16.8   to   12-May-2013/03:09:00.9 (UTC)
</pre>

== CASA Version ==

This guide has been written for CASA release 4.1.0. Please confirm your version before proceeding.

<source lang="python">
# In CASA
version = casadef.casa_version
print "You are using " + version
if (version < '4.1.0'):
    print "YOUR VERSION OF CASA IS TOO OLD FOR THIS GUIDE."
    print "PLEASE UPDATE IT BEFORE PROCEEDING."
else:
    print "Your version of CASA is appropriate for this guide."
</source>

==Initial Inspection==

We will eventually concatenate the six datasets used here into one large dataset.  However, we will keep them separate for now, as some of the steps to follow require individual datasets to be calibrated separately (namely, the sky/Tsys calibration and baseline subtraction).  We therefore start by defining an array "basename" that includes the names of the six files in chronological order. This will simplify the following steps by allowing us to loop through the files using a simple for-loop in python.  Remember that if you log out of CASA, you will have to re-issue this command.  We will remind you of this in the relevant sections by repeating the command at the start.

<source lang="python">
# In CASA
basename=['uid___A002_X60b415_X39a','uid___A002_X60b415_X6f7','uid___A002_X6218fb_X264', 'uid___A002_X6218fb_X425','uid___A002_X6321c5_X3a7','uid___A002_X6321c5_X5ca']
</source>

== Creating Single Dish data format ==

The raw data have been provided to you in the ASDM format. ASDM stands for ALMA Science Data Model. It is the native format of the data produced by the observatory. 

=== Create Measurement Sets ===

Before we can proceed to the calibration, we will need to convert those data to the CASA MS format. This is done simply with the task importasdm. For example:

<source lang="python">
#In CASA
importasdm(vis = 'uid___A002_X60b415_X39a')
</source>
Note: importasdm has an option singledish, which you may be tempted to use. It works, but it has some limitations (which will be removed in the future), so for now, we recommend not using it.

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.  

<source lang="python">
# In CASA
for name in basename:
        listobs(vis=name+'.ms')
</source>

Note that after cutting and pasting a for-loop you often have to press return several times to execute.
The output will be sent to the CASA [http://casa.nrao.edu/docs/userman/UserMansu41.html#UserMansu42.html logger].  
You will have to scroll up to see the individual output for each of the six datasets.  Here is an example of the most relevant output for the fifth file in the list.

These commands define a python list called "basename", which contains the name of all 6 MS files. 
The "for" loop executes for each element in basename, calling listobs and directing the output to a file called, e.g., "uid___A002_X60b415_X39a.ms.listobs.txt" for the first measurement set. 
You can browse through the listobs output as you would normally look at a text file (use emacs, vi, or another editor). You can also send the output to the terminal from inside of CASA. To do so type:

<source lang="python">
# In CASA
os.system('cat uid___A002_X60b415_X39a.ms.listobs.txt')
</source>

or

<source lang="python">
# In CASA
os.system('more uid___A002_X60b415_X39a.ms.listobs.txt')
</source>

CASA knows a few basic shell commands like 'cat', 'ls', and 'rm' but for more complex commands you will need to run them inside 'os.system("command")'. For more information see http://casa.nrao.edu/ .

Here is an example of the (abridged) output from {{listobs}} for the first dataset in the list, uid___A002_X60b415_X39a.ms. You would see this if you had specified '''verbose''' to be False in the listobs call:

<pre style="background-color: #fffacd;">
Observation: ALMA
Data records: 16588       Total integration time = 1302.91 seconds
   Observed from   12-May-2013/02:22:16.9   to   12-May-2013/02:43:59.8 (UTC)

   ObservationID = 0         ArrayID = 0
  Date        Timerange (UTC)          Scan  FldId FieldName           nRows   nUnflRows   SpwIds   Average Interval(s)    ScanIntent
  12-May-2013/02:22:16.3 - 02:22:42.8     1      0 M100                    900      0.00  [0, 1, 2, 3, 4, 5, 6, 7, 8]  [1.15, 0.48, 0.48, 0.48, 0.48, 0.48, 0.48, 0.48, 0.48] CALIBRATE_ATMOSPHE
RE#ON_SOURCE,CALIBRATE_WVR#ON_SOURCE
              02:23:24.3 - 02:25:11.4     2      0 M100                   1524      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:25:25.2 - 02:27:11.2     3      0 M100                   1522      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:27:25.1 - 02:29:11.0     4      0 M100                   1522      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:29:24.9 - 02:31:12.0     5      0 M100                   1524      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:31:25.8 - 02:33:11.8     6      0 M100                   1522      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:34:03.6 - 02:34:29.0     7      0 M100                    900      0.00  [0, 1, 2, 3, 4, 5, 6, 7, 8]  [1.15, 0.48, 0.48, 0.48, 0.48, 0.48, 0.48, 0.48, 0.48] CALIBRATE_ATMOSPHE
RE#ON_SOURCE,CALIBRATE_WVR#ON_SOURCE
              02:34:42.8 - 02:36:30.0     8      0 M100                   1524      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:36:43.8 - 02:38:29.8     9      0 M100                   1524      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:38:43.6 - 02:40:30.7    10      0 M100                   1524      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:40:44.5 - 02:42:30.5    11      0 M100                   1524      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
              02:42:44.4 - 02:44:00.4    12      0 M100                   1078      0.00  [0, 9, 10, 11, 12, 13, 14, 15, 16]  [1.15, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01, 1.01] OBSERVE_TAR
GET#OFF_SOURCE,CALIBRATE_WVR#OFF_SOURCE
           (nRows = Total number of rows per scan) 
Fields: 1
  ID   Code Name                RA               Decl           Epoch   SrcId    nRows  nUnflRows
  0    none M100                12:22:54.899040 +15.49.20.57200 J2000   0        16588       0.00
Spectral Windows:  (17 unique spectral windows and 2 unique polarization setups)
  SpwID  Name                           #Chans   Frame   Ch1(MHz)  ChanWid(kHz)  TotBW(kHz) BBC Num  Corrs  
  0      WVR#NOMINAL                         4   TOPO  184550.000   1500000.000   7500000.0       0  XX
  1      ALMA_RB_03#BB_1#SW-01#FULL_RES    128   TOPO  101942.187    -15625.000   2000000.0       1  XX  YY
  2      ALMA_RB_03#BB_1#SW-01#CH_AVG        1   TOPO  100926.562   1781250.000   1781250.0       1  XX  YY
  3      ALMA_RB_03#BB_2#SW-01#FULL_RES    128   TOPO  103757.337    -15625.000   2000000.0       2  XX  YY
  4      ALMA_RB_03#BB_2#SW-01#CH_AVG        1   TOPO  102741.712   1781250.000   1781250.0       2  XX  YY
  5      ALMA_RB_03#BB_3#SW-01#FULL_RES    128   TOPO  111814.962     15625.000   2000000.0       3  XX  YY
  6      ALMA_RB_03#BB_3#SW-01#CH_AVG        1   TOPO  112783.712   1781250.000   1781250.0       3  XX  YY
  7      ALMA_RB_03#BB_4#SW-01#FULL_RES    128   TOPO  113689.962     15625.000   2000000.0       4  XX  YY
  8      ALMA_RB_03#BB_4#SW-01#CH_AVG        1   TOPO  114658.712   1781250.000   1781250.0       4  XX  YY
  9      ALMA_RB_03#BB_1#SW-01#FULL_RES   4080   TOPO  101945.850      -488.281   1992187.5       1  XX  YY
  10     ALMA_RB_03#BB_1#SW-01#CH_AVG        1   TOPO  100949.756   1992187.500   1992187.5       1  XX  YY
  11     ALMA_RB_03#BB_2#SW-01#FULL_RES   4080   TOPO  103761.000      -488.281   1992187.5       2  XX  YY
  12     ALMA_RB_03#BB_2#SW-01#CH_AVG        1   TOPO  102764.906   1992187.500   1992187.5       2  XX  YY
  13     ALMA_RB_03#BB_3#SW-01#FULL_RES   4080   TOPO  111811.300       488.281   1992187.5       3  XX  YY
  14     ALMA_RB_03#BB_3#SW-01#CH_AVG        1   TOPO  112806.906   1992187.500   1992187.5       3  XX  YY
  15     ALMA_RB_03#BB_4#SW-01#FULL_RES   4080   TOPO  113686.300       488.281   1992187.5       4  XX  YY
  16     ALMA_RB_03#BB_4#SW-01#CH_AVG        1   TOPO  114681.906   1992187.500   1992187.5       4  XX  YY
Sources: 19
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
  0    M100                0     -              -            
  0    M100                17    -              -            
  0    M100                18    -              -            
  0    M100                1     -              -            
  0    M100                2     -              -            
  0    M100                3     -              -            
  0    M100                4     -              -            
  0    M100                5     -              -            
  0    M100                6     -              -            
  0    M100                7     -              -            
  0    M100                8     -              -            
  0    M100                9     100950         0            
  0    M100                10    100950         0            
  0    M100                11    102794.1       0            
  0    M100                12    102794.1       0            
  0    M100                13    112794.1       0            
  0    M100                14    112794.1       0            
  0    M100                15    114669.1       0            
  0    M100                16    114669.1       0            
Antennas: 2:
  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
                                                                     East         North     Elevation               x               y               z
  0    PM01  T704      12.0 m   -067.45.16.2  -22.53.22.1         42.8992     -520.1885       22.2159  2225113.044955 -5440122.820877 -2481517.728410
  1    PM04  T703      12.0 m   -067.45.16.2  -22.53.23.9         42.8809     -575.6904       21.7744  2225104.701420 -5440102.470120 -2481568.688227

</pre>

This output shows that three sources were observed in each data set: M100.

* '''M100''' are our science target. Note that the source corresponds to a number of individual fields (see the Field ID column). 
The output also shows that the data contain many spectral windows. Using the labeling scheme in the listobs above these are:

* '''spw 9''','''spw 11''','''spw 13''' and '''spw 15'''  hold our science data. These are "Frequency Domain Mode" (FDM) data with small (0.49 MHz) channel width and wide total bandwidth. As a result these have a lot of channels (4080). spw 15 holds the lower sideband (LSB) data and includes the CO(1-0) line. 
We will focus on these data.
* '''spw 1''','''spw 3''','''spw 5''' and '''spw 7''' hold lower a resolution processing ("Time Domain Mode", TDM) of the data from the same part of the spectrum (baseband). These data have only 128 channels across 2 GHz bandwidth and so have a much coarser channel spacing than the FDM data. 
These were used to generate the calibration tables that we include in the tarball but will not otherwise appear in this guide.

=== Create ASAP formats ===

We are now going to go through each of them with a bit more explanations. We will take the example of uid___A002_X6218fb_X264.ms.
Before starting, you need to know that most of the tasks that we will use are part of the ASAP package, which was incorporated into CASA. 
The ASAP package is using a different data format, so from a global point of view, what we are going to do is, first convert the MS to the ASAP format, then run the necessary calibration tasks, then convert the data back to the MS format. Another important difference with interferometric data reduction is that the calibration is performed directly on the dataset, we will not produce calibration tables and apply them at the end. An effort is on-going to update the SD routines so that this is done, that should be available soon, but until then, please remember that all SD calibration operations apply to the data directly, so you may want to always create a new dataset each time, so that you do not have to start all over again.

We will then convert the data to the ASAP format. We will use the routine sd.splitant for that. An outprefix has to be specified because the routine will create a dataset per antenna, taking the outprefix, and appending the antenna name and the format extension ('.asap').

<source lang="python">
# In CASA
sd.splitant(filename = 'uid___A002_X6218fb_X264.ms',
    outprefix = 'uid___A002_X6218fb_X264.ms',
    overwrite = True,
    freq_tolsr = True)
</source>

The reason for the option freq_tolsr=True is to convert the frequencies in the MS from TOPO to LSRK. This is an important setting, as due to current limitations, it is the only stage where this conversion can be done. Using freq_tolsr=False would keep the frame of the frequencies from the MS, and would force you to image the final cube in TOPO velocities. Another important aspect is for the baselining/line finding: if your observations have been obtained at different epochs, it may be easier to work on spectra with LSRK frequencies because then the line emissions of all spectra can be overlapped.


We have now two ASAP datasets, one for PM03 and one for PM04. As usual, we will first obtain information about the content of the datasets, using sdlist (equivalent of listobs).

<source lang="python">
# In CASA
sdlist(infile = 'uid___A002_X6218fb_X264.ms.PM03.asap',
    outfile = 'uid___A002_X6218fb_X264.ms.PM03.asap.sdlist')
  
sdlist(infile = 'uid___A002_X6218fb_X264.ms.PM04.asap',
    outfile = 'uid___A002_X6218fb_X264.ms.PM04.asap.sdlist')
</source>

Here is an example of the most relevant output for uid___A002_X6218fb_X264.ms.PM04.asap.sdlist.

<source lang="python">
# In CASA
os.system('more uid___A002_X6218fb_X264.ms.PM04.asap.sdlist')
</source>

<pre style="background-color: #fffacd;">
--------------------------------------------------------------------------------
 Scan Table Summary
--------------------------------------------------------------------------------
Project:       uid://A002/X5d9e5c/X42
Obs Date:      2013/04/28/04:10:19
Observer:      cvlahakis
Antenna Name:  ALMA//PM04@T703
Data Records:  15186 rows
Obs. Type:     CALIBRATE_ATMOSPHERE#ON_SOURCE,CALIBRATE_WVR#ON_SOURCE
Beams:         1   
IFs:           17  
Polarisations: 2   (linear)
Channels:      4080
Flux Unit:     K
Abscissa:      Channel
Selection:     none

Scan Source         Time range                           Int[s] Record SrcType FreqIDs MolIDs 
       Beam  Position (J2000)       
--------------------------------------------------------------------------------
   0 M100           2013/04/28/04:12:06.1 - 04:13:17.3   0.500364   594  [PSON:CALON, PSOFF:CALON] [0, 1, 2, 3, 4, 5, 6, 7, 8] [0]
       0      J2000 12:23:07.0 +15.51.15.9
   1 M100           2013/04/28/04:14:05.0 - 04:15:50.8   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.9 +15.51.17.4
   2 M100           2013/04/28/04:16:09.4 - 04:17:56.4   1.01628  1443  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.8 +15.51.19.1
   3 M100           2013/04/28/04:18:13.8 - 04:20:00.8   1.01628  1443  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.8 +15.51.20.6
   4 M100           2013/04/28/04:20:19.4 - 04:22:05.2   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.7 +15.51.22.2
   5 M100           2013/04/28/04:22:23.8 - 04:24:09.7   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.6 +15.51.23.7
   6 M100           2013/04/28/04:25:03.7 - 04:26:14.7   0.500364   594  [PSON:CALON, PSOFF:CALON] [0, 1, 2, 3, 4, 5, 6, 7, 8] [0]
       0      J2000 12:23:06.5 +15.51.25.6
   7 M100           2013/04/28/04:26:33.8 - 04:28:19.6   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.5 +15.51.26.7
   8 M100           2013/04/28/04:28:38.2 - 04:30:25.2   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.4 +15.51.28.1
   9 M100           2013/04/28/04:30:42.6 - 04:32:29.6   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.3 +15.51.29.5
  10 M100           2013/04/28/04:32:48.2 - 04:34:34.0   1.01619  1442  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.2 +15.51.30.9
  11 M100           2013/04/28/04:34:52.6 - 04:36:08.5   1.0162  1018  [PSOFF, PSON] [0, 9, 10, 11, 12, 13, 14, 15, 16] [0, 1, 2, 3, 4]
       0      J2000 12:23:06.2 +15.51.32.3
--------------------------------------------------------------------------------
FREQUENCIES: 9
   ID  IFNO   Frame   RefVal          RefPix Increment      Channels POLNOs
    0    0     LSRK     1.87675e+11    1.5        2.5e+09         4  [0]
    1    1     LSRK      1.0095e+11   63.5      -15625000       128  [0, 1]
    2    2     LSRK   1.0092656e+11      0   -1.78125e+09         1  [0, 1]
    3    3     LSRK   1.0276515e+11   63.5      -15625000       128  [0, 1]
    4    4     LSRK   1.0274171e+11      0   -1.78125e+09         1  [0, 1]
    5    5     LSRK   1.1280715e+11   63.5       15625000       128  [0, 1]
    6    6     LSRK   1.1278371e+11      0    1.78125e+09         1  [0, 1]
    7    7     LSRK   1.1468215e+11   63.5       15625000       128  [0, 1]
    8    8     LSRK   1.1465871e+11      0    1.78125e+09         1  [0, 1]
    9    9     LSRK      1.0095e+11 2039.5     -488281.25      4080  [0, 1]
   10   10     LSRK   1.0094976e+11      0 -1.9921875e+09         1  [0, 1]
   11   11     LSRK   1.0276515e+11 2039.5     -488281.25      4080  [0, 1]
   12   12     LSRK   1.0276491e+11      0 -1.9921875e+09         1  [0, 1]
   13   13     LSRK   1.1280715e+11 2039.5      488281.25      4080  [0, 1]
   14   14     LSRK   1.1280691e+11      0  1.9921875e+09         1  [0, 1]
   15   15     LSRK   1.1468215e+11 2039.5      488281.25      4080  [0, 1]
   16   16     LSRK   1.1468191e+11      0  1.9921875e+09         1  [0, 1]
--------------------------------------------------------------------------------
MOLECULES: 
   ID   RestFreq          Name           
    0   [] []
    1   [1.0095e+11] [Manual_window(ID=0)]
    2   [1.02794e+11] [Manual_window(ID=0)]
    3   [1.12794e+11] [Manual_window(ID=0)]
    4   [1.14669e+11] [CO_v_0_1_0(ID=3768098)]
--------------------------------------------------------------------------------
</pre>

== Calibration ==

About the calibration itself: the two main steps are 

<pre style="background-color: #fffacd;">

1. the calibration of the spectra into K, by applying the Tsys calibration and removing the signal from the OFF position

2. removing the baselines (i.e. subtracting the background emission, to keep only the line emission.)

</pre>

=== Tsys ===

Let's start by checking the Tsys solutions. We will use the gencal command used for interferometric data reduction. 
This will produce a CASA calibration table, which can be analysed similarly to previous guides '''[[M100 Band3 ACA 4.1#Tsys]]'''

<source lang="python">
# In CASA
gencal(vis = 'uid___A002_X6218fb_X264.ms',
    caltable = 'uid___A002_X6218fb_X264.ms.tsys',
    caltype = 'tsys')

plotbandpass(caltable='uid___A002_X6218fb_X264.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_X6218fb_X264.ms.tsys.plots.overlayTime/uid___A002_X6218fb_X264.ms.tsys') 
</source>

This sequence loops over all of our files and plots Tsys as a function of time for channel. In the call to {{plotcal}}:

* '''subplot'''=22 parameter sets up a 2 x 2 panel grid. 
* '''iteration''' tells {{plotcal}} to make a separate plot for each antenna.

For the spectral window association, we will use the routine tsysspwmap available directly in CASA.
<source lang="python">
# In CASA
from recipes.almahelpers import tsysspwmap
tsysmap = tsysspwmap(vis = 'uid___A002_X6218fb_X264.ms', tsystable = 'uid___A002_X6218fb_X264.ms.tsys')
</source>

tsysmap is a list of indices, with tsysmap[i] being the index of the Tsys spw to associate to the science spw of index i.

In the next step, we will do the actual preparation of the Tsys (i.e. re-sampling and re-indexing of the Tsys spw), using the library filltsys, also available directly in CASA.
<source lang="python">
# In CASA
import filltsys

for i in [9, 11, 13, 15]:
    filltsys.fillTsys('uid___A002_X6218fb_X264.ms.PM03.asap',
      specif = i,
      tsysif = tsysmap[i],
      mode = 'linear',
      extrap = True)
  
for i in [9, 11, 13, 15]:
    filltsys.fillTsys('uid___A002_X6218fb_X264.ms.PM04.asap',
      specif = i,
      tsysif = tsysmap[i],
      mode = 'linear',
      extrap = True)
</source>

This will loop through each science spw, re-sample the Tsys solutions associated to spw of index tsysmap[i] using a linear interpolation, allowing for extrapolation in case the science and Tsys spw do not perfectly match, and re-index it to spw of index i.
'''You will note that the SD tasks use the word 'if': this is equivalent to 'spw id' in interferometry tasks.'''

=== A Priori Flagging ===

We have now prepared the Tsys solutions for application. We have not applied them yet. We will first do some a-priori flagging, of the edge channels. This is similar to flagging edge channels in TDM interferometry datasets. In FDM interferometry datasets, these edge channels are not written out, so there is no need to flag anything. Here, we have an FDM SD dataset, produced with the second correlator (the ACA correlator), which does not excise them (yet).

Each spw covers the full baseband width (2GHz), so we will flag 120 channels on each side so as to keep only the center 3840 channels, similarly to FDM interferometry datasets.

<source lang="python">
# In CASA
sdflag(infile = 'uid___A002_X6218fb_X264.ms.PM03.asap',
    specunit = 'channel',
    iflist = [9, 11, 13, 15],
    maskflag = [[0, 119], [3960, 4079]],
    overwrite = True)
  
sdflag(infile = 'uid___A002_X6218fb_X264.ms.PM04.asap',
    specunit = 'channel',
    iflist = [9, 11, 13, 15],
    maskflag = [[0, 119], [3960, 4079]],
    overwrite = True)
</source>

=== Apply Calibration ===

Now is the step where we will actually calibrate the data. This is done with the task sdcal. This is a straight-forward operation, so no opportunity for tweaking. The calibration mode (calmode) shall be 'ps', as in Position Switching. The task will find automatically the OFF-position measurements. We need to specify the science spws (iflist) because they are the only ones that can be calibrated. We specify a different output file (outfile) so as to be able to come back to the original dataset if necessary.

<source lang="python">
# In CASA
sdcal(infile = 'uid___A002_X6218fb_X264.ms.PM03.asap',
    calmode = 'ps',
    iflist = [9, 11, 13, 15],
    scanaverage = False,
    timeaverage = False,
    polaverage = False,
    outfile = 'uid___A002_X6218fb_X264.ms.PM03.asap.cal',
    overwrite = True)

sdcal(infile = 'uid___A002_X6218fb_X264.ms.PM04.asap',
    calmode = 'ps',
    iflist = [9, 11, 13, 15],
    scanaverage = False,
    timeaverage = False,
    polaverage = False,
    outfile = 'uid___A002_X6218fb_X264.ms.PM04.asap.cal',
    overwrite = True)
</source>

Before proceeding to the next step, we can plot the calibrated spectra, using the sdplot task. The commands below will plot one spectrum per scan, spw and polarization. It is difficult to describe what a good spectrum looks like at this stage. What you should look for is outliers (i.e. spectra that differ from most, whether in shape or level).

<source lang="python">
# In CASA
for i in [9, 11, 13, 15]:
  sdplot(infile='uid___A002_X6218fb_X264.ms.PM03.asap.cal',
    iflist=[i], plottype='spectra', specunit='channel', scanaverage=True, stack='pol', panel='scan',
    outfile='uid___A002_X6218fb_X264.ms.PM03.asap.cal.plots/uid___A002_X6218fb_X264.ms.PM03.asap.cal.spectra.spw'+str(i)+'.png',
    overwrite = True)
  
for i in [9, 11, 13, 15]:
  sdplot(infile='uid___A002_X6218fb_X264.ms.PM04.asap.cal',
    iflist=[i], plottype='spectra', specunit='channel', scanaverage=True, stack='pol', panel='scan',
    outfile='uid___A002_X6218fb_X264.ms.PM04.asap.cal.plots/uid___A002_X6218fb_X264.ms.PM04.asap.cal.spectra.spw'+str(i)+'.png',
    overwrite = True)
</source>

=== Baseline Subtraction ===

We will now perform the second main step of the calibration: the baselining. This is done with the sdbaseline task.
In the commands below, the baseline fitting method is controlled by the parameters blfunc and order. Many fitting methods are available (’poly’,’chebyshev’,’cspline’,’sinusoid’, see help of sdbaseline task for more information). Here, we will do a simple linear fitting.

The parameter maskmode allows excluding portions of the spectra from the baseline fitting. This is mainly useful to exclude channels where there are line emissions (it could also be used to excluse the edge channels, in case they were not flagged beforehand). The channels can be specified as a list or chosen interactively. Another option is to use the line finder implemented in the sdbaseline task, using maskmode = 'auto'; then the parameters thresh and avg_limit can be used to tweak the line finding algorithm. (thresh is specified in sigma units, avg_limit is specified as a number of channels.)

<source lang="python">
# In CASA
sdbaseline(infile = 'uid___A002_X6218fb_X264.ms.PM03.asap.cal',
    iflist = [9, 11, 13, 15],
    maskmode = 'auto',
    thresh = 3.0,
    avg_limit = 8,
    blfunc = 'poly',
    order = 1,
    outfile = 'uid___A002_X6218fb_X264.ms.PM03.asap.cal.bl',
    overwrite = True)
  
sdbaseline(infile = 'uid___A002_X6218fb_X264.ms.PM04.asap.cal',
    iflist = [9, 11, 13, 15],
    maskmode = 'auto',
    thresh = 3.0,
    avg_limit = 8,
    blfunc = 'poly',
    order = 1,
    outfile = 'uid___A002_X6218fb_X264.ms.PM04.asap.cal.bl',
    overwrite = True)
</source>

We run again sdplot to check the output spectra, fully calibrated this time.

<source lang="python">
# In CASA
for i in [9, 11, 13, 15]:
  sdplot(infile='uid___A002_X6218fb_X264.ms.PM04.asap.cal.bl',
    iflist=[i], plottype='spectra', specunit='channel', scanaverage=True, stack='pol', panel='scan',
    outfile='uid___A002_X6218fb_X264.ms.PM04.asap.cal.bl.plots/uid___A002_X6218fb_X264.ms.PM04.asap.cal.bl.spectra.spw'+str(i)+'.png',
    overwrite = True)
  
for i in [9, 11, 13, 15]:
  sdplot(infile='uid___A002_X6218fb_X264.ms.PM03.asap.cal.bl',
    iflist=[i], plottype='spectra', specunit='channel', scanaverage=True, stack='pol', panel='scan',
    outfile='uid___A002_X6218fb_X264.ms.PM03.asap.cal.bl.plots/uid___A002_X6218fb_X264.ms.PM03.asap.cal.bl.spectra.spw'+str(i)+'.png',
    overwrite = True)
</source>

'''We have now entirely calibrated the data. Into Kelvin units. The conversion to Jy will be covered into the guide on combination.'''

== Prepare for Imaging==

=== Convert each ASAP dataset to an MS ===
Here, we will convert all of the calibrated asap dataset into measurement sets. The CASA task {{sdsave}} will do this.

<source lang="python">
#In CASA
sdsave(infile = 'uid___A002_X6218fb_X264.ms.PM03.asap.cal.bl',
    outfile = 'uid___A002_X6218fb_X264.ms.PM03.asap.cal.bl.ms',
    outform = 'MS2')
  
sdsave(infile = 'uid___A002_X6218fb_X264.ms.PM04.asap.cal.bl',
    outfile = 'uid___A002_X6218fb_X264.ms.PM04.asap.cal.bl.ms',
    outform = 'MS2')
</source>

=== Combine all executions to one MS ===
Concatenate all of the calibrated measurement sets into one for imaging.  The CASA task {{concat}} will do this.

<source lang="python">
#In CASA
os.system('rm -rf concat_m100.ms')
concat(vis='uid___A002_X60b415_X39a.ms.cal.split', 'uid___A002_X60b415_X6f7.ms.cal.split', 'uid___A002_X6218fb_X264.ms.cal.split', 'uid___A002_X6218fb_X425.ms.cal.split', 'uid___A002_X6321c5_X3a7.ms.cal.split', 'uid___A002_X6321c5_X5ca.ms.cal.split'],
       concatvis='concat_m100.ms',
       freqtol='10MHz')
</source>

The individual calibrated MSs have slightly different observing frequencies, although the rest frequencies are the same.  The freqtol parameter sets the tolerance for considering whether the different spectral windows from the input datasets should be output as the same spectral window ID.

== Image the Total Power Data ==

Run listobs on the total power data to see what spw contains the CO

<source lang="python">
#In CASA
os.system('rm -rf concat_m100.ms.listobs')
listobs(vis='concat_m100.ms',listfile='concat_m100.ms.listobs')
</source>

Spectral window SPWID=3 contains the 115.27 GHz line, so we image this window.  
The task {{sdimaging}} will do this.

<source lang="python">
#In CASA
os.system('rm -rf TP_CO_cube')
sdimaging(infile='concat_m100.ms',
          field=0,spw=3,
          specunit='km/s',restfreq='115.271204GHz',
          dochannelmap=True,
          nchan=70,start=1400,step=5,
          gridfunction='gjinc',imsize=[50,50],
          cell=['10arcsec','10arcsec'],
          phasecenter = 'J2000 12h22m54.9 +15d49m15'
          outfile='TP_CO_cube')
</source>

The restfreq parameter must be specified when using "km/s" as the units, as in this case.
Start and step parameters are specified in units that the user chooses for specunit.  The numbers
here are chosen so that the resulting image has the same number of channels, velocity range and 
channel width as the 7m and 12m array images.

===Gridding Function===  
The gridfunction is the weighting function that is used to grid the observed flux to individual pixels in the image. 

<pre style="background-color: #fffacd;">
"SF":  a spheroidal function, which minimizes aliasing effects.  

"BOX":  a pillbox function, which defaults to a kernel box size of 1 pixel.  

"PB" (primary beam): assumes an Airy disk, corresponding to an antenna with 10.7m diameter, the effective diameter of an ALMA 12m antenna.

"GAUSS":  a gaussian, and its size can be defined by additional subparameters (truncate and gwidth).  

"GJINC": a gaussian convolved with the Bessel function, and can minimize the broadening of the effective beam.  

</pre>

Any of the functions which require the observing frequency for determining the beam size will read the frequency from the dataset, and the user can use the default.
The cell size should be chosen so that it is about 1/3 to 1/4 of the FWHM of the effective beam.

== Image Analysis : Moment Maps ==

Next we will make moment maps for the CO(1-0) emission: Moment 0 is the integrated intensity; Moment 1 is the intensity weighted velocity field; and Moment 2 is the intensity weighted velocity dispersion. 

Above we determined the rms noise levels for M100 mosaics in a line-free and a line-bright channel. 
We want to limit the channel range of the moment calculations to those channels with significant emission. One good way to do this is to open the cube in the viewer overlaid with 3-sigma contours, with sigma corresponding to the line-free rms. 

For moment 0 (integrated intensity) maps you do not typically want to set a flux threshold because this will tend to noise bias your integrated intensity.

<source lang="python">
# In CASA
os.system('rm -rf M100_SD_cube.image.mom*')
immoments(imagename = 'M100_SD_cube.image',
         moments = [0],
         axis = 'spectral',
         chans = '1~24',
         outfile = 'M100_SD_cube.image.mom0')
</source>

For higher order moments it is very important to set a conservative flux threshold. Typically something like 6sigma, using sigma from a bright line channel works well. We do this with the '''mask''' parameter in the commands below. When making multiple moments, {{immoments}} appends the appropriate file name suffix to the value of '''outfile'''. 

<source lang="python">
# In CASA
os.system('rm -rf M100_SD_cube.image.mom*')
immoments(imagename = 'M100_SD_cube.image',
         moments = [1],
         axis = 'spectral',
         chans = '1~24',
         includepix = [0.018, 1.0],
         outfile = 'M100_SD_cube.image.mom1')
</source>

== Export data as fits ==

If you want to analyze the data using another software package it is easy to convert from CASA format to FITS. 

<source lang="python">
# In CASA
os.system('rm -rf M100_SD_*.fits')
exportfits(imagename='M100_SD_cube.image', fitsimage='M100_SD_cube.image.fits')
exportfits(imagename='M100_SD_cube.image.mom0', fitsimage='M100_SD_mom0.fits')
</source>

Although "FITS format" is supposed to be a standard, in fact most packages expect slightly different things from a FITS image. If you are having difficulty, try setting '''velocity=T''' and/or '''dropstokes=T'''.