NGC3256Band3 for CASA 3.3: Difference between revisions

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==Overview==
[[Category:ALMA]][[Category:Calibration]][[Category:Spectral Line]]
[To be written by Eric]


==Retrieving the Data==
==Science Target Overview==
[[File:OpticalImageNGC3256.jpg|200px|thumb|right|HST image of NGC3256 (credit: NASA, ESA, the Hubble Heritage Team (STScI/AURA)-ESA/Hubble Collaboration and A. Evans (University of Virginia, Charlottesville/NRAO/Stony Brook University)]]
[[File:CO2-1_image_SMA.jpg|200px|thumb|right|SMA map of CO (2–1) emission in the center of NGC 3256 (Sakamoto, Ho & Peck, 2006)]]


The data were taken in six different datasets over two consecutive nights: April 16-17, 2011.  There are three datasets for April 16th and three for April 17th.  Here we provide you with "starter" datasets, where we have taken the raw data in ALMA Science Data Model (ASDM) format and converted them to CASA Measurement Sets (MS). We did this using the {{importasdm}} task in CASA.
The luminous infrared galaxy NGC 3256 is the brightest galaxy within ~40 Mpc. This galaxy, which is in the later stages of a merger between two gas-rich progenitors, hosts an extreme central starburst that can be seen across a wide range of wavelengths but emits most strongly in the far infrared (Smith & Harvey 1996)Hubble Space Telescope optical imaging has revealed hundreds of bright young clusters in the galactic center (Trancho et al. 2007). There is also strong evidence for a superwind in NGC 3256, indicating strong starburst-driven blow-out of the interstellar medium (Heckman et al. 2000). Imaging in the infrared, radio and X-rays has shown that NGC 3256 has two distinct nuclei aligned in the north-south direction and separated by 5 arcsec, or 850 pc, on the sky. The southern nucleus is highly obscured, rendering it invisible in the optical.  


[What else are we going to do to the data we provide?]
Because of its proximity and the fact that it is observed nearly face-on, NGC 3256 is an ideal target to study merger-induced starbursts in the local Universe. In fact, NGC 3256 could be regarded as the southern sky equivalent of Arp 220, the archetype of infrared-luminous merging galaxies.


Along with the Measurement Sets, we also provide some tables that you will need for the calibration. These include the System Temperature (Tsys) tables, which contain corrections for atmospheric opacity, and Water Vapor Radiometer (WVR) tables, which contain the atmospheric phase corrections determined by the water vapor radiometers on each antenna.
Neutral gas in this galaxy was first studied by English et al (2003), who detected two HI tidal tails that extend up to 50 kpc. High-resolution observations of carbon-monoxide (CO 2-1) in NGC 3256 were made by Sakamoto et al. (2006) using the Submillimeter Array (SMA). This study revealed a large disk of molecular gas (r > 3 kpc) in the center of the merger, with a strong gas concentration toward the double nucleus. This gas disk rotates around a point between the two nuclei. In addition, high-velocity molecular gas was discovered at the galaxy's center, with velocities up to 420 km/s offset from the systemic velocity of the galaxy.


You can download the data here:
==ALMA Data Overview==
ALMA Science verification data on NGC3256 in Band 3 were taken in six different
datasets over two consecutive nights: April 16-17, 2011. There are three datasets
for April 16th and three for April 17th. These Band 3 observations utilized all four
available basebands, which are associated with four different spectral windows: two
in the Upper Sideband (USB) and two in the Lower Sideband (LSB). The first spectral
window is centered on the CO(1-0) emission line in the galaxy NGC 3256 and is our
highest frequency spectral window. There is one additional spectral window in the
Upper Side Band (USB), and there are two spectral windows in the Lower Side Band
(LSB). These additional spectral windows are used to measure the continuum emission
in the galaxy and may contain other emission lines as well. Each spectral window
has a total bandwidth of 2 GHz divided over 128 channels, for a channel width of
15.625 MHz, corresponding to about 40 km/s. Online Hanning smoothing was applied to
the data, resulting in a spectral resolution that is twice the channel separation.
For the antenna configuration that was used during these observations, the angular
resolution is expected to be about 6.5".


[Provide link to the raw .ms files in tar'd, gzip'd format]
Due to unfortunate weather conditions during the days planned for these
observations, the data were taken at Band 3 although no previous interferometric
CO(1-0) observations of this galaxy exist. Casoli et al. (1990) observed the CO(1-0)
line with the SEST 15 single dish telescope and were just able to measure a velocity
field with 22" resolution. Interferometric observations were first made with the SMA
in the CO(2-1) line by Sakamoto, Ho & Peck (2006).  Because those observations were
made at a  higher frequency, the angular resolution is higher (~2") than that of the
ALMA observations shown here, taken in a very compact configuration. Nonetheless, it
is possible to make a direct comparison of the distribution and velocity of the
CO(2-1) and (1-0) gas by looking, for example, at the south-western clump and the
north-eastern 'arm', which are consistent in both data sets.


Once the download has finished, unpack the file:
We thank the following people for suggesting NGC3256 for ALMA Science Verification:
<source lang="python">
Kazushi Sakamoto, Satoki Matsushita.
# In a terminal outside CASA
tar -xvf ngc3256band3.tgz
</source>


[Also provide links to the calibrated data (but maybe not here...maybe better at end of calibration page?)]
==Obtaining the Data==


==Initial Inspection and ''A priori '' Flagging==
To download the data, click on the region closest to your location:
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 (specifically, the application of the Tsys and WVR tables).  We therefore start by defining an array "basename" that includes the names of the six files. This will simplify the following steps by allowing us to loop through the files using a simple for-loop in python. 


<source lang="python">
[http://almascience.nrao.edu/almadata/sciver/NGC3256 North America]
# In CASA
basename=['uid___A002_X1d54a1_X5','uid___A002_X1d54a1_X174','uid___A002_X1d54a1_X2e3',
'uid___A002_X1d5a20_X5','uid___A002_X1d5a20_X174','uid___A002_X1d5a20_X330']
</source>


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.
[http://almascience.eso.org/almadata/sciver/NGC3256 Europe]


<source lang="python">
[http://almascience.nao.ac.jp/almadata/sciver/NGC3256 East Asia]
# In CASA
for name in basename:
        listobs(vis=name+'.ms')
</source>


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 first file in the list.
Here you will find three gzipped tar files which, after unpacking, will create three directories:


<pre style="background-color: #fffacd;">
*'''NGC3256_Band3_UnCalibratedMSandTablesForReduction''' - Here we provide you with "starter" datasets, where we have taken the raw data in ALMA Science Data Model (ASDM) format and converted them to CASA Measurement Sets (MS).  We did this using the {{importasdm}} task in CASAAlong with the raw data, we also provide some tables that you will need for the calibration which cannot currently be generated inside of CASA (for Early Science, these tables will either be pre-applied or supplied with the data).  
Fields: 3
  ID  Code Name        RA            Decl          Epoch  SrcId nVis 
  0    none 1037-295    10:37:16.0790 -29.34.02.8130 J2000  0    38759 
  1    none Titan        00:00:00.0000 +00.00.00.0000 J2000  1    16016 
  2    none NGC3256      10:27:51.6000 -43.54.18.0000 J2000  2    151249
  (nVis = Total number of time/baseline visibilities per field)  
Spectral Windows:  (9 unique spectral windows and 2 unique polarization setups)
  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)TotBW(kHz)  Ref(MHz)    Corrs 
  0          4 TOPO  184550      1500000    7500000    183300      I 
  1        128 TOPO  113211.988 15625      2000000    113204.175 XX  YY 
  2          1 TOPO  114188.55  1796875    1796875    113204.175  XX  YY 
  3        128 TOPO  111450.813  15625      2000000    111443      XX  YY 
  4          1 TOPO  112427.375  1796875    1796875    111443      XX  YY 
  5        128 TOPO  101506.187  15625      2000000    101514      XX  YY 
  6          1 TOPO  100498.375  1796875    1796875    101514      XX  YY 
  7        128 TOPO  103050.863  15625      2000000    103058.675  XX  YY 
  8          1 TOPO  102043.05  1796875    1796875    103058.675  XX  YY 
Sources: 48
  ID  Name        SpwId RestFreq(MHz)  SysVel(km/s)  
  0    1037-295    0    -              -           
  0    1037-295    9    -              -           
  0    1037-295    10    -              -           
  0    1037-295    11    -              -           
  0    1037-295    12    -              -           
  0    1037-295    13    -              -           
  0    1037-295    14    -              -           
  0    1037-295    15    -              -           
  0    1037-295    1    -              -           
  0    1037-295    2    -              -           
  0    1037-295    3    -              -           
  0    1037-295    4    -              -           
  0    1037-295    5    -              -           
  0    1037-295    6    -              -           
  0    1037-295    7    -              -           
  0    1037-295    8    -              -           
  1    Titan        0    -              -           
  1    Titan        9    -              -           
  1    Titan        10    -              -           
  1    Titan        11    -              -           
  1    Titan        12    -              -           
  1    Titan        13    -              -           
  1    Titan        14    -              -           
  1    Titan        15    -              -           
  1    Titan        1    -              -           
  1    Titan        2    -              -           
  1    Titan        3    -              -           
  1    Titan        4    -              -           
  1    Titan        5    -              -           
  1    Titan        6    -              -           
  1    Titan        7    -              -           
  1    Titan        8    -              -           
  2    NGC3256      0    -              -           
  2    NGC3256      9    -              -           
  2    NGC3256      10    -              -           
  2    NGC3256      11    -              -           
  2    NGC3256      12    -              -           
  2    NGC3256      13    -              -           
  2    NGC3256      14    -              -           
  2    NGC3256      15    -              -           
  2    NGC3256      1    -              -           
  2    NGC3256      2    -              -           
  2    NGC3256      3    -              -           
  2    NGC3256      4    -              -           
  2    NGC3256      5    -              -           
  2    NGC3256      6    -              -           
  2    NGC3256      7    -              -           
  2    NGC3256      8    -              -           
Antennas: 7:
  ID  Name  Station  Diam.    Long.        Lat.       
  0    DV04  J505      12.0 m  -067.45.18.0  -22.53.22.8 
  1    DV06  T704      12.0 m  -067.45.16.2  -22.53.22.1 
  2    DV07  J510      12.0 m  -067.45.17.8  -22.53.23.5 
  3    DV08  T703      12.0 m  -067.45.16.2  -22.53.23.9 
  4    DV09  N602      12.0 m  -067.45.17.4  -22.53.22.
  5    PM02  T701      12.0 m  -067.45.18.8  -22.53.22.2 
  6    PM03  J504      12.0 m  -067.45.17.0  -22.53.23.0
</pre>


This output shows that three fields were observed: 1037-295, Titan, and NGC3256.  Field 0 (1037-295) will serve as the gain calibrator and bandpass calibrator; field 1 (Titan) will serve as the flux calibrator; and field 2 (NGC3256) is, of course, the science target. 
*'''NGC3256_Band3_CalibratedData''' - The fully-calibrated uvdata, ready for imaging and self-calibration


Note that there are more than four SpwIDs even though the observations were set up to have four spectral windows.  The spectral line data themselves are found in spectral windows 1,3,5,7, which have 128 channels each. The first one (spw 1) is centered on the CO(1-0) emission line in the galaxy NGC 3256 and is our highest frequency spectral window. There is one additional spectral window (spw 3) in the Upper Side Band (USB), and there are two spectral windows (spw 5 and 7) in the Lower Side Band (LSB). These additional spectral windows are used to measure the continuum emission in the galaxy, and may contain other emission lines as well.
*'''NGC3256_Band3_ReferenceImages''' - The final continuum and spectral line images


Spectral windows 2,4,6,8 contain channel averages of the data in spectral windows 1,3,5,7, respectively. These are not useful for the offline data reduction. Spectral window 0 contains the WVR data.  You may notice that there are additional SpwIDs listed in the "Sources" section which are not listed in the "Spectral Windows" section. These spectral windows are reserved for the WVRs of each antenna (seven in our case). At the moment, all WVRs point to spw 0, which contains nominal frequencies. The additional spectral windows (spw 9-15) are therefore not used and can be ignored.
To see which files you will need, read on below. The downloads to your local computer will take some time, so you may wish to begin them now.


Another important thing to note is that the position of Titan is listed as 00:00:00.0000 +00.00.00.0000.  This is due to the fact that for ephemeris objects, the positions are currently not stored in the asdm. This will be handled correctly in the near future, but at present, we have to fix this offline.  We will correct the coordinates below by running the procedure fixplanet.  
'''NOTE: CASA 3.3 or later is required to follow this guide.'''  For more information on obtaining the latest version of CASA, see [http://casa.nrao.edu/ http://casa.nrao.edu].


Seven antennas we used for the dataset listed above.  Note that numbering in python always begins with "0", so the antennas have IDs 0-6.  To see what the antenna configuration looked like at the time of the this observation, we will use the task {{plotants}}.
==NGC3256 Data Reduction Tutorial==


[[File:Uid___A002_X1d54a1_X5_plotants.png|200px|thumb|right|plotants output]]
In this tutorial, or "casaguide", we will guide you step-by-step through the reduction of the ALMA science verification data on NGC3256 and its subsequent imaging. This casaguide consists of two parts:
<source lang="python">
# In CASA
plotants(vis=basename[0]+'.ms', figfile=basename[0]+'_plotants.png')
</source>


This will plot the antenna configuration on your screen as well as save it under the specified filename for future reference.  This will be important later on when we need to choose a reference antenna, since the reference antenna should be close to the center of the array (as well as stable and present for the entire observation)
1) '''[[NGC3256 Band3 - Calibration]]'''


If you repeat the plotants command for the other five datasets, you will see that there is an additional antenna (DV10) present on the second day of observations.  Other than that, the configuration stays constant during the course of the observations.
2) '''[[NGC3256 Band3 - Imaging]]'''


==== Flagging ====
To complete the Calibration section of the tutorial, you will need the data in the first directory: NGC3256_Band3_UnCalibratedMSandTablesForReduction.  For those wishing to skip the calibration section and proceed to Imaging, we also provide the fully-calibrated data in the NGC3256_Band3_CalibratedData directory. Finally, we provide the final continuum and spectral line images in the NGC3256_Band3_ReferenceImages directory.
The first editing we will do is some ''a priori'' flagging with {{flagdata}} and {{flagautocorr}}. We will start by flagging the shadowed data and the autocorrelation data:


<source lang="python">
For a similar tutorial on the reduction of ALMA Band 7 data on TW Hydra, see the casaguide '''[[TWHydraBand7]]'''.
# In CASA
for name in basename:
flagdata(vis=name+'.ms', flagbackup = F, mode = 'shadow')
flagautocorr(vis=name+'.ms')
</source>


There are a number of scans in the data that were used by the online system for pointing calibration. These scans are no longer needed, and we can flag them easily with {{flagdata}} by selecting on 'intent':
==How to use this casaguide==


<source lang="python">
For both portions of the guide, we will provide you with the full CASA commands needed to carry out each step.
# In CASA
for name in basename:
        flagdata(vis=name+'.ms', mode='manualflag', flagbackup = F, intent='*POINTING*')
</source>


Similarly, we can flag the scans corresponding to atmospheric calibration:
<source lang="python">
<source lang="python">
# In CASA
# In CASA
for name in basename:
The commands you need to execute
        flagdata(vis=name+'.ms', mode='manualflag', flagbackup = F, intent='*ATMOSPHERE*')
will be displayed in regions
like this.
</source>
</source>


We will then store the current flagging state for each dataset using the {{flagmanager}}:
Simply copy and paste the commands in order into your CASA terminal.  You may also type the commands in by hand if desired, but be mindful of typos.  Note that you may need to hit Enter twice in order for the process to start running. Also note that copying and pasting multiple commands at a time may not work, so only copy and paste the contents of one region at a time. 
<source lang="python">
# In CASA
for name in basename:
        flagmanager(vis = name+'.ms', mode = 'save', versionname = 'Apriori')
</source>


We will continue with some initial flagging/corrections specific to these datasets. For uid___A002_X1d54a1_X174.ms there is a outlying feature in spw=7, antenna DV04. This corresponds to scans 5 and 9, so we flag those data:
'''To learn how to extract the CASA commands into an executable python script, click [http://casaguides.nrao.edu/index.php?title=Extracting_scripts_from_these_tutorials here].'''


<source lang="python">
Occasionally we will also show output to the CASA logger:
# In CASA
flagdata(vis='uid___A002_X1d54a1_X174.ms', mode='manualflag',
antenna='DV04', flagbackup = F, scan='5,9', spw='7')
</source>


Antenna DV07 shows large delays for the first three datasets.  We correct this by calculating a K-type delay calibration table with {{gencal}}. The parameters are the delays measured in nanoseconds, first cycling over polarization product, and then over spectral window (thus giving eight numbers in total).  Before creating these tables, make sure to delete any existing versions.
<pre style="background-color: #fffacd;">
This output will be displayed
<source lang="python">
in regions like this.
# In CASA
</pre>
for i in range(3): # loop over the first three ms's
name=basename[i]
os.system('rm -rf '+name+'_del.K')
gencal(vis=name+'.ms', caltable=name+'_del.K',
caltype='sbd', antenna='DV07', pol='X,Y', spw='1,3,5,7',
        parameter=[0.99, 1.10, -3.0, -3.0, -3.05, -3.05, -3.05, -3.05])
</source>
 
The delay values were simply estimated by eye. The purpose here is to get the phases approximately flat as a function of frequency. Any additional phase variations will be corrected for later when we do the bandpass calibration.
 
Note that when you run the gencal command above, CASA may generate the warning "No scr col generation!!!"  This just means that there is no field association in the tables generated, so that you can apply them to any of the fields in the observation.  This is not important, so you can ignore the warning.
 
We will apply these K tables to the data in the next section.
 
==WVR Correction and Tsys Calibration==
 
We will now apply the delay correction table and the WVR calibration tables to the data with the task {{applycal}}. We do this in two steps.  First we will cycle over the three datasets from the first day of observations, because we have to correct the delay error for DV07 for those data. For the last three datasets (i.e. those taken during the second day), we do not need to correct the delays, so we just apply the WVR tables.  In the call to applycal, we will specify interpolation="nearest".  This is important for the WVR corrections, and it doesn't make a difference for the delay corrections because they have no time dependence.
 
<source lang="python">
# In CASA
for i in range(3): # loop over the first three data sets
name=basename[i]
applycal(vis=name+'.ms', flagbackup=F, spw='1,3,5,7',
interp=['nearest','nearest'], gaintable=[name+'_del.K',name+'.W'])
 
for i in range(3,6): # loop over the last three data sets
name=basename[i]
applycal(vis=name+'.ms', flagbackup=F, spw='1,3,5,7',
interp='nearest', gaintable=name+'.W')
</source>
 
Now we split out the corrected_data column of the datasets with the task {{split}}. We give the resulting datasets the extension "_K_WVR" to indicate that the delay tables and WVR tables have been applied in the data column, and we specify spectral windows 0-8 to get rid of the "WVR placeholder" spectral windows. Again, we are careful to remove any previous versions of the split ms's before running the split command.
 
<source lang="python">
# In CASA
for name in basename:
os.system('rm -rf '+name+'_K_WVR.ms*')
split(vis=name+'.ms', outputvis=name+'_K_WVR.ms',
datacolumn='corrected', spw='0~8')
</source>
 
Next we do the Tsys calibration.  Tsys measurements correct for the atmospheric opacity (to first-order) and allow the calibration sources to be measured at elevations that differ from the science target.  The Tsys tables for these datasets were provided with the downloadable data.  We will start by inspecting them with the task {{plotcal}}:
 
[[File:tsys_per_spwuid___A002_X1d54a1_X5.png|200px|thumb|right|Tsys plot]]
<source lang="python">
# In CASA
for name in basename:
plotcal(caltable='tsys_'+name+'.cal', xaxis='freq', yaxis='amp',
                spw='1,3,5,7', subplot=221, overplot=False,
                iteration='spw', plotrange=[0, 0, 40, 180], plotsymbol='.',
                figfile='tsys_per_spw'+name+'.png')
</source>
 
Note that we only plot the spectral windows with the spectral line data.  In addition to plotting on your screen, the above command will also produce a plot file (png) for each of the six datasets.  An example plot is shown to the right for the first dataset. 
 
Aside from the large amplitudes in the edge channels (which we will handle below), the plots look acceptable. We will therefore apply the Tsys tables with {{applycal}}:  We do this for each field separately so that the appropriate calibration data are applied to the right fields.  The "field" parameter specifies the field to which we will apply the calibration, and the "gainfield" parameter specifies the field from which you wish to take the calibration solutions from the gaintable. 
 
<source lang="python">
# In CASA
for name in basename:
for field in ['Titan','1037*','NGC*']:
applycal(vis=name+'_K_WVR.ms', spw='1,3,5,7', flagbackup=F, field=field, gainfield=field,
interp='nearest', gaintable=['tsys_'+name+'.cal'])
</source>
 
We then once again split out the corrected_data column, this time only retaining spectral windows 1,3,5,7. This will get rid of the extraneous spectral windows, including the channel averaged spectral windows and spw 0, which is the one for the WVR data. 
 
<source lang="python">
# In CASA
for name in basename:
os.system('rm -rf '+name+'_line.ms*')
split(vis=name+'_K_WVR.ms', outputvis=name+'_line.ms',
datacolumn='corrected', spw='1,3,5,7')
</source>
 
The WVR and Tsys tables are now applied in the data column of the new measurement sets. These datasets have the extension "_line" to indicate that they only contain the spectral line data and no longer the "channel average" spectral windows. These measurement sets therefore have four spectral windows, with IDs 0-3.
 
Now that we have applied the Tsys calibration and WVR corrections, we can concatenate the six individual data sets into one big measurement set. We define an array "comvis" that contains the names of the measurement sets we wish to concatenate, and then we run the task {{concat}}.
 
<source lang="python">
# In CASA
comvis=[]
for name in basename:
comvis.append(name+'_line.ms')
 
os.system('rm -rf ngc3256_line.ms*')
concat(vis=comvis, concatvis='ngc3256_line.ms')
</source>
 
==Additional Data Inspection==
 
Now that the data are concatenated into one dataset, we will do some additional inspection with {{plotms}}.  First we will plot amplitude versus channel, averaging over time and baselines in order to speed up the plotting process. 
 
[[File:amp_vs_chan_ngc3256_line.png|200px|thumb|right|Amp vs. Chan]]
<source lang="python">
# In CASA
plotms(vis='ngc3256_line.ms', xaxis='channel', yaxis='amp',
      averagedata=T, avgbaseline=T, avgtime='1e8', avgscan=T)
</source>
 
From this plot we see that the edge channels have abnormally high amplitudes.  We will use {{flagdata}} to remove the edge channels from both sides of the bandpass:
 
<source lang="python">
# In CASA
flagdata(vis = 'ngc3256_line.ms', flagbackup = F, spw = ['*:0~10','*:125~127'])
</source>
 
Next, we will look at amplitude versus time, averaging over all channels and colorizing by field.  Since the observations take place over two days, you will need to zoom in to examine the data in more detail.  In particular, note the difference in Titan's amplitude between the two days and the change in amplitude during the second day.
 
<source lang="python">
# In CASA
plotms(vis='ngc3256_line.ms', xaxis='time', yaxis='amp',
      averagedata=T, avgchannel='128', coloraxis='field')
</source>
 
Titan is our primary flux calibrator. However, for the second day of observations, Titan had moved to close to Saturn, and Saturn's rings moved into the primary beam. Another way to see this is to plot amplitude versus uv-distance and colorize by scan:
 
[[File:amp_vs_uvdistTitan_ngc3256_line.png|200px|thumb|right|Amp vs uvdist]]
<source lang="python">
# In CASA
plotms(vis='ngc3256_line.ms', xaxis='uvdist', yaxis='amp', field='1',
      averagedata=T, avgchannel='128', avgtime='1e8', coloraxis='scan')
</source>
 
If you use the "Mark a region" and "Locate" tools in {{plotms}}, you will see the signature of a bright, resolved source during the latter three (last day's) scans.  We will therefore need to flag the Titan scans for the second day:
 
<source lang="python">
# In CASA
flagdata(vis = 'ngc3256_line.ms', flagbackup = F,
timerange='>2011/04/16/12:00:00', field='Titan')
</source>
 
Next, we will fix the position of Titan in the combined dataset. Recall that the position of the Titan field is currently set to 00:00:00.0000 +00.00.00.0000.  The following procedure will replace this with the actual position observed by the telescopes and, at the same time, it will recalculate the uvw coordinates:
 
<source lang="python">
# In CASA
execfile(os.getenv("CASAPATH").split(' ')[0]+"/lib/python2.6/recipes/fixplanets.py")
 
fixplanets('ngc3256_line.ms', 'Titan', True)
</source>
 
Continue to inspect the data with {{plotms}}, plotting different axes and colorizing by the different parameters.  Don't forget to average the data if possible to speed the plotting process.  You will find the following:
*Baselines with DV07 have very high amplitudes in spw 3, correlation YY
*Baselines with DV08 have very low amplitudes in spw 3, correlation YY, but only for the last observation
*Baselines with PM03 have low amplitudes at 2011/04/17/02:15:00 for spw 0
*Baselines with PM03 have low amplitudes at 2011/04/16/04:15:15 for spw 2 and 3
 
We flag the bad data with the following commands:
 
<source lang="python">
# In CASA
flagdata(vis='ngc3256_line.ms', flagbackup=F, spw='3',
correlation='YY', mode='manualflag', selectdata=T,
antenna='DV07', timerange='')
 
flagdata(vis='ngc3256_line.ms', flagbackup=F, spw='3',
correlation='YY', mode='manualflag', selectdata=T,
antenna='DV08', timerange='>2011/04/17/03:00:00')
 
flagdata(vis='ngc3256_line.ms', flagbackup=F, spw='0',
mode='manualflag', selectdata=T, antenna='PM03',
timerange='2011/04/17/02:15:00~02:15:50')
 
flagdata(vis='ngc3256_line.ms', flagbackup=F, spw='2,3',
mode='manualflag', selectdata=T, antenna='PM03',
timerange='2011/04/16/04:13:50~04:18:00')
</source>
 
==Bandpass Calibration==
 
We are now ready to begin the bandpass calibration.  First, we will inspect the bandpass calibrator by plotting the phase and amplitude as a function of frequency. We use avgscan=T and avgtime='1E6' to average in time over all scans, and we specify coloraxis='baseline' to colorize by baseline. 
 
<source lang="python">
# In CASA
plotms(vis='ngc3256_line.ms', xaxis='freq', yaxis='phase', selectdata=True,
field='1037*', avgtime='1E6', avgscan=T, coloraxis='baseline', iteraxis='antenna')
 
plotms(vis='ngc3256_line.ms', xaxis='freq', yaxis='amp', selectdata=True, spw='*:10~120',
field='1037*', avgtime='1E6', avgscan=T, coloraxis='baseline', iteraxis='antenna')
</source>
 
[WHAT TO SAY ABOUT THESE PLOTS?]
 
Before we do the actual bandpass calibration, we first need to run {{gaincal}} on the bandpass calibrator to determine phase-only gain solutions. We will use solint='int' for the solution interval, which means that one gain solution will be determined for every integration time.  This will correct for any phase variations in the bandpass calibrator as a function of time, a step which will prevent decorrelation of the vector-averaged bandpass solutions.  We will then apply these solutions on-the-fly when we run {{bandpass}}. 
 
We will use the average of channels 40 to 80 to increase our signal-to-noise in the determination of the antenna-based phase solutions.  Averaging over a subset of channels near the center of the bandpass is acceptable when the phase variation as a function of channel is small, which it is here.  For our reference antenna, we choose PM03. We call the output calibration table "ngc3256.G1".
 
<source lang="python">
# In CASA
gaincal(vis = 'ngc3256_line.ms', caltable = 'ngc3256.G1', spw = '*:40~80', field = '1037*',
        selectdata=T, solint= 'int', refant = 'PM03', calmode = 'p')
</source>
 
We then check the time variations of the phase solutions with {{plotcal}}. We will plot the XX and YY polarization products separately and make different subplots for each of the spectral windows. This is done by setting the "iteration" parameter to "spw" and specifying subplot=221. By setting the parameter "figfile" to a non-blank value, it will also generate png files of the plots. 
 
<source lang="python">
# In CASA
plotcal(caltable = 'ngc3256.G1', xaxis = 'time', yaxis = 'phase',
poln='X', plotsymbol='o', plotrange = [0,0,-180,180], iteration = 'spw',
figfile='phase_vs_time_XX.G1.png', subplot = 221)
 
plotcal(caltable = 'ngc3256.G1', xaxis = 'time', yaxis = 'phase',
poln='Y', plotsymbol='o', plotrange = [0,0,-180,180], iteration = 'spw',
figfile='phase_vs_time_YY.G1.png', subplot = 221)
</source>
 
Now that we have a first measurement of the phase variations as a function of time, we can determine the bandpass solutions with {{bandpass}}. We will apply the phase calibration table on-the-fly with the parameter "gaintable".
 
<source lang="python">
# In CASA
bandpass(vis = 'ngc3256_line.ms', caltable = 'ngc3256.B1', gaintable = 'ngc3256.G1',
field = '1037*', minblperant=3, minsnr=1, solint='inf',
bandtype='B', fillgaps=1, refant = 'PM03', solnorm = F)
</source>
 
*caltable = 'ngc3256.B1': output bandpass calibration table
*gaintable = 'ngc3256.G1': gain calibration table to apply
*minblperant=3: Minimum number of baselines required per antenna for each solve
*minsnr=1: Minimum SNR for solutions
*solint='inf': This setting, combined with the default combine='scan', sets the solution interval to the entire observation
*bandtype='B': The default type of bandpass solution, which does a channel by channel solution for each specified spw
*fillgaps=1: Interpolate channel gaps 1 channel wide
*solnorm=T:  Normalize the bandpass amplitudes and phases of the corrections to unity  [THAT WAS A REMNANT OF ME EXPERIMENTING> I USE T IN MY SCRIPT AS WELL. SORRY. I UPDATED THE FIGURE ]
 
We then plot the bandpass solutions with the following commands:
 
[[File:Bandpass.B1.png|200px|thumb|right|Bandpass Solutions]]
<source lang="python">
# In CASA
plotcal(caltable = 'ngc3256.B1', xaxis='freq', yaxis='phase', spw='',
subplot=212, overplot=False, plotrange = [0,0,-70,70],
plotsymbol='.', timerange='')
 
plotcal(caltable = 'ngc3256.B1', xaxis='freq', yaxis='amp', spw='',
subplot=211, overplot=False,
figfile='bandpass.B1.png', plotsymbol='.', timerange='')
</source>
 
[PERHAPS APPLY THE SOLUTIONS AND SHOW PLOTS HERE?]
 
== Gain Calibration ==
 
The first step is to set the flux density for Titan using the task {{setjy}}.  We will use the Butler-JPL-Horizons 2010 model, for which the flux density of Titan is 296 mJy at 103 GHz (spw 3). 
 
<source lang="python">
# In CASA
setjy(vis='ngc3256_line.ms', field='Titan', standard='Butler-JPL-Horizons 2010')
</source>
 
Now we will do a new gain calibration, this time applying the bandpass calibration solutions on-the-fly:
 
<source lang="python">
# In CASA
gaincal(vis = 'ngc3256_line.ms', caltable = 'ngc3256.G2', calmode = 'ap',
        spw = '*:30~90', field = '1037*, Titan', solint= 'inf', solnorm=F,
        refant = 'PM03', gaintable = ['ngc3256.B1'])
</source>
 
*caltable = 'ngc3256.G2': the output gain calibration table
*calmode = 'ap': To solve for both amplitude and phase
*spw='*:30~90': to select all spectral windows, but only channels 30-90 in each [...WHY?]
*solint='inf': Together with the default for the "combine" parameter, this setting will solve for one solution per scan
*solnorm=F: We do not want to normalize the solutions to unity since we wish to relate the measured amplitudes of the secondary calibrator (1037-295) to the flux calibrator (Titan)
*gaintable = ['ngc3256.B1']: We apply the bandpass calibration on-the-fly
 
[ YOU ARE JUST SOLVING FOR A&P AT THE SAME TIME?  YOU DON'T SOLVE FOR P FIRST USING A SHORTER TIME INTERVAL, THEN USE THAT TO DERIVE THE AMPLITUDE SOLUTIONS PER SCAN?  MAYBE IT DOESN'T MAKE A BIG DIFFERENCE HERE? - thought it would not make much of a difference, but please try if you have time. Otherwise just leave as is.]
 
[ANOTHER QUESTION: WHY DO YOU RESTRICT THE CHANNEL RANGE ABOVE?]
 
Now we will examine the amplitude and phase solutions as a function of time, iterating on spectral window and plotting the XX and YY correlations separately for clarity. Zoom in on the GUI to examine the plots in more detail.  You can also use the "Mark Region" and "Locate" buttons on the toolbar to identify points. 
 
<source lang="python">
# In CASA
plotcal(caltable = 'ngc3256.G2', xaxis = 'time', yaxis = 'phase',
poln='X', plotsymbol='o', plotrange = [0,0,-180,180], iteration
= 'spw', figfile='phase_vs_time_XX.G2.png', subplot = 221)
 
plotcal(caltable = 'ngc3256.G2', xaxis = 'time', yaxis = 'phase',
poln='Y', plotsymbol='o', plotrange = [0,0,-180,180], iteration
= 'spw', figfile='phase_vs_time_YY.G2.png', subplot = 221)
 
plotcal(caltable = 'ngc3256.G2', xaxis = 'time', yaxis = 'amp',
poln='X', plotsymbol='o', plotrange = [], iteration = 'spw',
figfile='amp_vs_time_XX.G2.png', subplot = 221)
 
plotcal(caltable = 'ngc3256.G2', xaxis = 'time', yaxis = 'amp',
poln='Y', plotsymbol='o', plotrange = [], iteration = 'spw',
figfile='amp_vs_time_YY.G2.png', subplot = 221)
</source>
 
[THESE PLOTS DONT LOOK THAT CLEAN TO ME - I SEE SOME STRAY POINTS.  I CAN'T TELL YOU WHAT THEY ARE RIGHT NOW BECAUSE MY INTERNET CONNECTION IS WOEFULLY SLOW.]
 
Finally, we will bootstrap the flux density of the secondary calibrator from that of Titan using the task {{fluxscale}}:
 
<source lang="python">
# In CASA
fluxscale( vis='ngc3256_line.ms', caltable='ngc3256.G2',
        fluxtable='ngc3256.G2.flux', reference='Titan', transfer='1037*')
</source>
 
Note that we previously flagged the Titan scans from the second day due to contamination from nearby Saturn's rings.  We have therefore used the Titan scans from the first day alone to flux calibrate both days' observations.  This would not always be an acceptable solution; however, in this case, examination of the measured amplitudes for the phase calibrator over both days indicate that the flux scale is relatively stable. 
 
We find that the flux density of 1037-295 is 1.8 Jy in all four spectral windows, which agrees very well with the 3mm measurements from the ATCA and OVRO of a few years ago.  [...REFERENCE?]
 
==Applying the calibrations ==
 
Now we will use {{applycal}} to apply the bandpass and gaincal tables that we generated in the previous sections. In addition to applying the solutions to the science target, we will also apply them to the secondary calibrator in order to check the quality of the calibration. 
 
<source lang="python">
# In CASA
applycal(vis='ngc3256_line.ms', field='NGC*,1037*',
        gaintable=['ngc3256.G2.flux','ngc3256.B1'], gainfield = ['1037*', '1037*'],
        interp='nearest', flagbackup=F)
</source>
 
*gaintable=['ngc3256.G2.flux','ngc3256.B1']: We apply the gaincal table with amplitude and phase solutions, and the bandpass table
*gainfield = ['1037*', '1037*']: We use the solutions from the secondary calibrator (1037-295) in both tables
*interp='nearest': We opt for interpolation mode "nearest" because...[WHY?**]
*flagbackup=F: We do not back up the state of the flags before applying calibration
 
Let's now use {{plotms}} to examine the corrected amplitude of NGC3256 as a function of frequency:
 
[[File:Amp_vs_freqNGC3256corr.png|200px|thumb|right|Amp vs Freq]]
<source lang="python">
# In CASA
plotms(vis='ngc3256_line.ms', xaxis='freq', yaxis='amp',
ydatacolumn='corrected', selectdata=True, field='NGC*',
averagedata=True, avgchannel='', avgtime='10000s',
avgscan=True, avgbaseline=T, coloraxis='spw')
</source>


Use the "Zoom" tool to zoom in on the different spectral windows.  (Note that spw 2-3 are on the left).  There are three emission lines in spectral windows 0-1. There is no emission in spw 2 and 3.  [LOOKS LIKE THERE ARE STILL SOME BAD CHANNELS ON THE EDGE OF SPW 2-3.]
For a brief introduction to the different ways CASA can be run, see the [[EVLA_Spectral_Line_Calibration_IRC%2B10216#How_to_Use_This_casaguide]] pageFor further help getting started with CASA, see [[Getting_Started_in_CASA]].


There are some additional bad data points, which we will flag with {{flagdata}}. [DID YOU FIND THESE POINTS USING THE ABOVE PLOT? I THINK IT WOULD BE GOOD TO FLAG THINGS AFTER THE PLOT WHERE YOU DISCOVER THEM]


<source lang="python">
[[User:Mzwaan|Martin Zwaan, Jacqueline Hodge]] 07:18 UT, 31 May 2011
# In CASA
{{Checked 3.3.0}}
flagdata(vis='ngc3256_line.ms', mode='manualflag',
timerange='2011/04/16/04:13:35~04:13:45', flagbackup = F)
tget(flagdata)
timerange='2011/04/16/05:21:13~05:21:19'
flagdata()
timerange='2011/04/16/04:16:40~04:16:49'
flagdata()
</source>
 
Note that in the above command sequence, we utilize the CASA function [http://casa.nrao.edu/docs/userman/UserMansu36.html#x44-430001.3.5.6 tget].  This function retrieves the last input values for the function specified.
 
At this point, we will image the secondary calibrator as a check of our calibration.  We do this using the task {{clean}}, after first removing any previous versions of the images that may exist in our directory.
 
<source lang="python">
# In CASA
os.system('rm -rf phasecal_cont*')
clean(vis='ngc3256_line.ms', imagename='phasecal_cont',
field='1037*', spw='*:20~120', mode='mfs', niter=1000,
        mask=[126, 126, 130,130], imsize=256,
        cell='1arcsec', weighting='briggs', robust=0.0)
</source>
 
*imagename='phasecal_cont': the base name of the output images
*spw='*:20~120': We image all spectral windows, ignoring the outermost channels of each
*mode='mfs': the default mode, which produces one image from all the specified data combined
*niter=1000: maximum number of clean iterations
*mask=[126, 126, 130,130]: Limits the clean component placement to the region of the source
*imsize=256, cell='1arcsec': Chosen to appropriately sample the resolution element and cover the primary beam
*weighting='briggs', robust=0: a weighting scheme that offers a good compromise between sensitivity and resolution
 
Once the imaging of the secondary calibrator is complete, we will generate some statistics on the image using the task {{imstat}}:
 
<source lang="python">
# In CASA
calstat=imstat(imagename='phasecal_cont.image', region='', box='160,50,210,210')
rms=(calstat['rms'][0])
print '>> rms in phase calibrator image: '+str(rms)
calstat=imstat(imagename='phasecal_cont.image', region='')
peak=(calstat['max'][0])
print '>> Peak in phase calibrator image: '+str(peak)
print '>> Dynamic range in phase calibrator image: '+str(peak/rms)
</source>
 
Here, we have used the "box" parameter in the first call of imstat to find the image rms in a region away from the strong central point source.  The image dynamic range in the calibrator image is ~2500.  [HMM, I ONLY GET 385.  I GUESS I MISSED A STEP SOMEWHERE...]  We will then look at the image of the secondary calibrator with {{imview}}. 
 
<source lang="python">
# In CASA
imview(raster={'file': 'phasecal_cont.image', 'colorwedge':T,
        'range':[-0.004, 0.250], 'scaling':-2.5, 'colormap':'Rainbow 2'},
        out='phasecal_map.png', zoom=1)
</source>
 
This command rasters phasecal_cont.image and outputs the file phasecal_map.png.  It uses the Rainbow 2 colomap scheme and includes a colorwedge on the plot.  The "range" and "scaling" parameters have been chosen to bring out the weaker features in the map. 
 
[MARTIN, CAN I SEE YOUR MAP HERE?]
 
 
Applycal on Titan. Use the phase solution on Titan this time.  [WOULDN'T IT BE BETTER TO DO THIS WHEN WE DO THE OTHER APPLYCALS, AND THEREFORE DO THEM ALL AT ONCE?]
 
<source lang="python">
# In CASA
applycal(vis='ngc3256_line.ms', flagbackup=F, field='Titan',
interp='nearest', gainfield = ['Titan', '1037*'],
gaintable=['ngc3256.G2.flux','ngc3256.B1'])
</source>
 
Image the amplitude calibrator (Titan)
<source lang="python">
# In CASA
os.system('rm -rf ampcal_cont*')
clean( vis="ngc3256_line.ms", imagename="ampcal_cont", field="Titan",
spw="0:20~120,1:20~120,2:20~120,3:20~120", selectdata=T,
mode="mfs", niter=500, gain=0.1, psfmode="clark",
interactive=False, mask=[126, 126, 130,130], imsize=256,
cell="1arcsec", weighting="briggs", robust=0.0)
</source>
 
Get some statistics on the ampcal image
 
<source lang="python">
# In CASA
calstat=imstat(imagename="ampcal_cont.image",region="",box="160,50,210,210")
rms=(calstat['rms'][0])
print ">> rms in amp calibrator image: "+str(rms)
calstat=imstat(imagename="ampcal_cont.image",region="")
peak=(calstat['max'][0])
print ">> Peak in amp calibrator image: "+str(peak)
print ">> Dynamic range in amp calibrator image: "+str(peak/rms)
</source>
 
Image dynamic range in calibrator image ~64
 
<source lang="python">
# In CASA
imview(raster={'file': 'ampcal_cont.image', 'colorwedge':T,
      'range':[-0.020, 0.250], 'scaling':-2.5, 'colormap':
      'Rainbow 2'},
      out='ampcal_map.png', zoom=1)
</source>
 
== Continuum image of the galaxy==
 
[SHOULD THIS START A NEW PAGE, LIKE HOW THE EVLA TUTORIAL ON 3C391 IS SPLIT INTO CALIBRATION AND IMAGING?]
 
Split out the science target
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_line_target.ms*')
split(vis='ngc3256_line.ms', outputvis='ngc3256_line_target.ms',
field='NGC*')
</source>
 
Clean the continuum image
 
<source lang="python">
# In CASA
os.system('rm -rf ngc3256.cont*')
clean( vis="ngc3256_line_target.ms", imagename="ngc3256_cont",
field='NGC*', spw="0:20~53;71~120,1:70~120,2:20~120,3:20~120",
selectdata=T, mode="mfs", niter=500, gain=0.1,
psfmode="clark", mask=[118,119,147,138], interactive=False,
imsize=256, cell="1arcsec", weighting="briggs", robust=0.0)
</source>
 
<source lang="python">
# In CASA
calstat=imstat(imagename="ngc3256_cont.image",region="",box="160,50,210,210")
rms=(calstat['rms'][0])
print ">> rms in continuum image: "+str(rms)
calstat=imstat(imagename="ngc3256_cont.image",region="")
peak=(calstat['max'][0])
print ">> Peak in continuum image: "+str(peak)
print ">> Dynamic range in continuum image: "+str(peak/rms)
</source>
 
Image dynamic range is around 34. Peak flux is ~6.7 mJy
 
<source lang="python">
# In CASA
imview(raster={'file': 'ngc3256_cont.image', 'colorwedge':T,
      'range':[-0.0003, 0.005], 'scaling':-1, 'colormap':
      'Rainbow 2'},
      out='ngc3256_cont.png', zoom=2)
</source>
 
# Do some phase-only self-cal on the continuum image.
# First use a solution interval of 15 mins
 
<source lang="python">
# In CASA
gaincal(vis="ngc3256_line_target.ms", field='NGC*',
    caltable="ngc3256_cont_900.Gp",
    spw="0:20~53;71~120,1:70~120,2:20~120,3:20~120",
    selectdata=True, solint='900s', refant='PM03', calmode='p',
    minblperant=3)
</source>
 
<source lang="python">
# In CASA
plotcal(caltable = 'ngc3256_cont_900.Gp', xaxis = 'time', yaxis =
'phase', poln='X', plotsymbol='o', plotrange = [0,0,-180,180],
iteration = 'spw', figfile='phase_vs_time_XX_900_Gp.png',
subplot = 221)
 
plotcal(caltable = 'ngc3256_cont_900.Gp', xaxis = 'time', yaxis =
'phase', poln='Y', plotsymbol='o', plotrange = [0,0,-180,180],
iteration = 'spw', figfile='phase_vs_time_YY_900_Gp.png',
subplot = 221)
</source>
 
Phase-only self-cal solutions look good.
 
<source lang="python">
# In CASA
applycal(vis='ngc3256_line_target.ms', interp='nearest',
gaintable=['ngc3256_cont_900.Gp'])
</source>
 
Make a new continuum map
 
<source lang="python">
# In CASA
os.system('rm -rf ngc3256.cont_sc1*')
clean( vis="ngc3256_line_target.ms", imagename="ngc3256_cont_sc1",
spw="0:20~53;71~120,1:70~120,2:20~120,3:20~120", selectdata=T,
mode="mfs", niter=500, gain=0.1, psfmode="clark",
mask=[118,119,147,138], interactive=False, imsize=256,
cell="1arcsec", weighting="briggs", robust=0.0)
</source>
 
<source lang="python">
# In CASA
calstat=imstat(imagename="ngc3256_cont_sc1.image",region="",box="160,50,210,210")
rms=(calstat['rms'][0])
print ">> rms in continuum image: "+str(rms)
calstat=imstat(imagename="ngc3256_cont_sc1.image",region="")
peak=(calstat['max'][0])
print ">> Peak in continuum image: "+str(peak)
print ">> Dynamic range in continuum image: "+str(peak/rms)
</source>
 
Continuum image has improved a lot. Dynamic range is ~110
Peak flux is ~9 mJy
 
<source lang="python">
# In CASA
imview(raster={'file': 'ngc3256_cont_sc1.image', 'colorwedge':T,
      'range':[-0.0003, 0.007], 'scaling':-1, 'colormap':
      'Rainbow 2'},
      out='ngc3256_cont_sc1.png', zoom=2)
</source>
 
== Line images of the galaxy==
 
We split to apply the latest self-cal tables
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_line_target_sc.ms*')
split(vis='ngc3256_line_target.ms', outputvis='ngc3256_line_target_sc.ms')
</source>
 
 
Subtract the continuum
 
<source lang="python">
# In CASA
uvcontsub(vis = 'ngc3256_line_target_sc.ms',
  fitspw="0:20~53;71~120,1:70~120,2:20~120,3:20~120", solint ='inf',
  fitorder = 1, fitmode = 'subtract')
</source>
 
Clean the CO line emission
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_line_CO.*')
clean(vis="ngc3256_line_target_sc.ms", imagename="ngc3256_line_CO",
outframe='LSRK', spw="0:48~78", start='', nchan=31, width='',
restfreq='115.271201800GHz', selectdata=T, mode="channel",
niter=500, gain=0.1, psfmode="clark", mask=[53,50,87,83],
interactive=True, imsize=128, cell="1arcsec",
weighting="briggs", robust=0.0)
</source>
 
 
Make the moment maps of the CO (1-0) emission
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_CO1-0.mom.*')
immoments(imagename="ngc3256_line_CO.image", moments=[0,1],
chans="5~24", box="38,38,90,90", axis="spectral",
includepix=[0.045, 10000], outfile="ngc3256_CO1-0.mom")
</source>
 
Clean the CN high line emission
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_line_CNhi.*')
clean(vis="ngc3256_line_target_sc.ms", imagename="ngc3256_line_CNhi",
outframe='LSRK', spw="1:50~76", start='', nchan=27, width='',
restfreq='113.49097GHz', selectdata=T, mode="channel",
niter=500, gain=0.1, psfmode="clark", mask=[53,50,87,83],
interactive=True, imsize=128, cell="1arcsec",
weighting="briggs", robust=0.0)
</source>
 
Make the moment maps of the CN (high) emission
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_CNhi.mom.*')
immoments( imagename="ngc3256_line_CNhi.image", moments=[0,1],
chans="5~18", axis="spectral",box="38,38,90,90",
includepix=[0.005, 10000], outfile="ngc3256_CNhi.mom")
</source>
 
Clean the CN low emission
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_line_CNlo.*')
clean( vis="ngc3256_line_target_sc.ms", imagename="ngc3256_line_CNlo",
outframe='LSRK', spw="1:29~54", start='', nchan=26, width='',
restfreq='113.18666GHz', selectdata=T, mode="channel",
niter=300, gain=0.1, psfmode="clark", mask=[53,50,87,83],
interactive=True, imsize=128, cell="1arcsec",
weighting="briggs", robust=0.0)
</source>
 
Make the moment maps of the CN (low) emission
<source lang="python">
# In CASA
os.system('rm -rf ngc3256_CNlo.mom.*')
immoments( imagename="ngc3256_line_CNlo.image", moments=[0,1],
chans="8~18", axis="spectral", box="38,38,90,90",
includepix=[0.003, 10000], outfile="ngc3256_CNlo.mom")
</source>
 
 
Make images of the CO(1-0) emission
 
<source lang="python">
# In CASA
imview(contour={'file': 'ngc3256_CO1-0.mom.integrated','range': []},
      raster={'file': 'ngc3256_CO1-0.mom.weighted_coord','range': [2630,2920],'colorwedge':T,
      'colormap': 'Rainbow 2'},
      out='CO_velfield.png')
</source>
 
<source lang="python">
# In CASA
imview(contour={'file': 'ngc3256_CO1-0.mom.weighted_coord','levels': [2650,2700,2750,2800,2850,2900],'base':0,'unit':1},
      raster={'file': 'ngc3256_CO1-0.mom.integrated','colorwedge':T,
      'colormap': 'Rainbow 2'},
      out='CO_map.png')
</source>
 
Make images of the CN high emission
 
<source lang="python">
# In CASA
imview(contour={'file': 'ngc3256_CNhi.mom.integrated','range': []},
      raster={'file': 'ngc3256_CNhi.mom.weighted_coord','range': [2630,2920],'colorwedge':T,
      'colormap': 'Rainbow 2'},
      out='CNhi_velfield.png')
</source>
 
<source lang="python">
# In CASA
imview(contour={'file': 'ngc3256_CNhi.mom.weighted_coord','levels': [2650,2700,2750,2800,2850,2900],'base':0,'unit':1},
      raster={'file': 'ngc3256_CNhi.mom.integrated','colorwedge':T,
      'colormap': 'Rainbow 2'},
      out='CNhi_map.png')
</source>
 
Make images of the CN low emission
 
<source lang="python">
# In CASA
imview(contour={'file': 'ngc3256_CNlo.mom.integrated','range': []},
      raster={'file': 'ngc3256_CNlo.mom.weighted_coord','range': [2630,2920],'colorwedge':T,
      'colormap': 'Rainbow 2'},
      out='CNlo_velfield.png')
</source>
 
<source lang="python">
# In CASA
imview(contour={'file': 'ngc3256_CNlo.mom.weighted_coord','levels': [2650,2700,2750,2800,2850,2900],'base':0,'unit':1},
      raster={'file': 'ngc3256_CNlo.mom.integrated','colorwedge':T,
      'colormap': 'Rainbow 2'},
      out='CNlo_map.png')
</source>

Latest revision as of 14:57, 26 April 2012


Science Target Overview

HST image of NGC3256 (credit: NASA, ESA, the Hubble Heritage Team (STScI/AURA)-ESA/Hubble Collaboration and A. Evans (University of Virginia, Charlottesville/NRAO/Stony Brook University)
SMA map of CO (2–1) emission in the center of NGC 3256 (Sakamoto, Ho & Peck, 2006)

The luminous infrared galaxy NGC 3256 is the brightest galaxy within ~40 Mpc. This galaxy, which is in the later stages of a merger between two gas-rich progenitors, hosts an extreme central starburst that can be seen across a wide range of wavelengths but emits most strongly in the far infrared (Smith & Harvey 1996). Hubble Space Telescope optical imaging has revealed hundreds of bright young clusters in the galactic center (Trancho et al. 2007). There is also strong evidence for a superwind in NGC 3256, indicating strong starburst-driven blow-out of the interstellar medium (Heckman et al. 2000). Imaging in the infrared, radio and X-rays has shown that NGC 3256 has two distinct nuclei aligned in the north-south direction and separated by 5 arcsec, or 850 pc, on the sky. The southern nucleus is highly obscured, rendering it invisible in the optical.

Because of its proximity and the fact that it is observed nearly face-on, NGC 3256 is an ideal target to study merger-induced starbursts in the local Universe. In fact, NGC 3256 could be regarded as the southern sky equivalent of Arp 220, the archetype of infrared-luminous merging galaxies.

Neutral gas in this galaxy was first studied by English et al (2003), who detected two HI tidal tails that extend up to 50 kpc. High-resolution observations of carbon-monoxide (CO 2-1) in NGC 3256 were made by Sakamoto et al. (2006) using the Submillimeter Array (SMA). This study revealed a large disk of molecular gas (r > 3 kpc) in the center of the merger, with a strong gas concentration toward the double nucleus. This gas disk rotates around a point between the two nuclei. In addition, high-velocity molecular gas was discovered at the galaxy's center, with velocities up to 420 km/s offset from the systemic velocity of the galaxy.

ALMA Data Overview

ALMA Science verification data on NGC3256 in Band 3 were taken in six different datasets over two consecutive nights: April 16-17, 2011. There are three datasets for April 16th and three for April 17th. These Band 3 observations utilized all four available basebands, which are associated with four different spectral windows: two in the Upper Sideband (USB) and two in the Lower Sideband (LSB). The first spectral window is centered on the CO(1-0) emission line in the galaxy NGC 3256 and is our highest frequency spectral window. There is one additional spectral window in the Upper Side Band (USB), and there are two spectral windows in the Lower Side Band (LSB). These additional spectral windows are used to measure the continuum emission in the galaxy and may contain other emission lines as well. Each spectral window has a total bandwidth of 2 GHz divided over 128 channels, for a channel width of 15.625 MHz, corresponding to about 40 km/s. Online Hanning smoothing was applied to the data, resulting in a spectral resolution that is twice the channel separation. For the antenna configuration that was used during these observations, the angular resolution is expected to be about 6.5".

Due to unfortunate weather conditions during the days planned for these observations, the data were taken at Band 3 although no previous interferometric CO(1-0) observations of this galaxy exist. Casoli et al. (1990) observed the CO(1-0) line with the SEST 15 single dish telescope and were just able to measure a velocity field with 22" resolution. Interferometric observations were first made with the SMA in the CO(2-1) line by Sakamoto, Ho & Peck (2006). Because those observations were made at a higher frequency, the angular resolution is higher (~2") than that of the ALMA observations shown here, taken in a very compact configuration. Nonetheless, it is possible to make a direct comparison of the distribution and velocity of the CO(2-1) and (1-0) gas by looking, for example, at the south-western clump and the north-eastern 'arm', which are consistent in both data sets.

We thank the following people for suggesting NGC3256 for ALMA Science Verification: Kazushi Sakamoto, Satoki Matsushita.

Obtaining the Data

To download the data, click on the region closest to your location:

North America

Europe

East Asia

Here you will find three gzipped tar files which, after unpacking, will create three directories:

  • NGC3256_Band3_UnCalibratedMSandTablesForReduction - Here we provide you with "starter" datasets, where we have taken the raw data in ALMA Science Data Model (ASDM) format and converted them to CASA Measurement Sets (MS). We did this using the importasdm task in CASA. Along with the raw data, we also provide some tables that you will need for the calibration which cannot currently be generated inside of CASA (for Early Science, these tables will either be pre-applied or supplied with the data).
  • NGC3256_Band3_CalibratedData - The fully-calibrated uvdata, ready for imaging and self-calibration
  • NGC3256_Band3_ReferenceImages - The final continuum and spectral line images

To see which files you will need, read on below. The downloads to your local computer will take some time, so you may wish to begin them now.

NOTE: CASA 3.3 or later is required to follow this guide. For more information on obtaining the latest version of CASA, see http://casa.nrao.edu.

NGC3256 Data Reduction Tutorial

In this tutorial, or "casaguide", we will guide you step-by-step through the reduction of the ALMA science verification data on NGC3256 and its subsequent imaging. This casaguide consists of two parts:

1) NGC3256 Band3 - Calibration

2) NGC3256 Band3 - Imaging

To complete the Calibration section of the tutorial, you will need the data in the first directory: NGC3256_Band3_UnCalibratedMSandTablesForReduction. For those wishing to skip the calibration section and proceed to Imaging, we also provide the fully-calibrated data in the NGC3256_Band3_CalibratedData directory. Finally, we provide the final continuum and spectral line images in the NGC3256_Band3_ReferenceImages directory.

For a similar tutorial on the reduction of ALMA Band 7 data on TW Hydra, see the casaguide TWHydraBand7.

How to use this casaguide

For both portions of the guide, we will provide you with the full CASA commands needed to carry out each step.

# In CASA
The commands you need to execute 
will be displayed in regions 
like this.

Simply copy and paste the commands in order into your CASA terminal. You may also type the commands in by hand if desired, but be mindful of typos. Note that you may need to hit Enter twice in order for the process to start running. Also note that copying and pasting multiple commands at a time may not work, so only copy and paste the contents of one region at a time.

To learn how to extract the CASA commands into an executable python script, click here.

Occasionally we will also show output to the CASA logger:

This output will be displayed 
in regions like this.

For a brief introduction to the different ways CASA can be run, see the EVLA_Spectral_Line_Calibration_IRC+10216#How_to_Use_This_casaguide page. For further help getting started with CASA, see Getting_Started_in_CASA.


Martin Zwaan, Jacqueline Hodge 07:18 UT, 31 May 2011

Last checked on CASA Version 3.3.0.