View source for VLA Flagging Intro Tutorial

== Notes on CASA ==

<b>This CASA Guide is for Version 6.5.4 of CASA.</b> If you are using a later version of CASA and this is the most recent available guide, then you should be able to use most, if not all, of this tutorial. This guide is meant to be completed using the monolithic CASA and not modular CASA as the GUI may not work correctly otherwise. 

There are a number of possible ways to run CASA, described in more detail in [[Getting Started in CASA]]. In this tutorial we would like you to use either (or both) of the following methods so that you can familiarize yourself with the CASA software:

* Interactive: examining task inputs. In this mode, one types '''taskname''' to load the task, '''inp''' to examine the inputs, and '''go''' once those inputs have been set to your satisfaction. Allowed inputs are shown in blue and bad inputs are colored red. The input parameters themselves are changed one by one, e.g., ''selectdata=True''. Screenshots of the inputs to various tasks used in the data reduction below are provided, to illustrate which parameters need to be set. More detailed help can be obtained on any task by typing '''help ''taskname'''''. Once a task is run, the set of inputs is stored and can be retrieved via '''tget ''taskname'''''; subsequent runs will overwrite the previous '''tget''' file.

* Pseudo-interactive: task function calls. In this mode, all of the desired inputs to a task are provided at once inn the CASA command line. This tutorial is made up of such calls, which were developed by looking at the inputs for each task and deciding what needed to be changed from default values. For task function calls, only parameters that you want to be different from their defaults need to be set.

This tutorial is largely self-paced. Any time you have a question, or something doesn't look right or you are unsure of, please do summon one of the tutors present in the room.

== Overview ==

<div style="text-align: justify;">
This CASA guide covers online data flagging, shadowing, zero-clipping, and quacking. It also covers auto-flagging RFI (Radio Frequency Interference) via TFCrop (Time-Frequency Crop) and rflag.

We will be utilizing data taken, with the Karl G. Jansky Very Large Array, of [http://simbad.u-strasbg.fr/simbad/sim-id?Ident=SNR+G055.7%2B03.4&NbIdent=1&Radius=2&Radius.unit=arcmin&submit=submit+id G055.7+3.4.], which is a supernova remnant. The data were taken on August 23, 2010 in the first D-configuration for which the new wideband capabilities of the WIDAR (Wideband Interferometric Digital ARchitecture) correlator were available. The 8-hour long session included all available 1 GHz of bandwidth in L-band, from 1&ndash;2 GHz in frequency., although in this guide we will use dataset composed of only 4 spectral windows (128 MHz bandwidth each). 

The guide will often reference the CASA documentation archives which are available [https://casadocs.readthedocs.io/en/stable/ online].

== Obtaining the Data ==

A copy of the data can be downloaded from [http://casa.nrao.edu/Data/EVLA/SNRG55/SNR_G55_10s.tar.gz http://casa.nrao.edu/Data/EVLA/SNRG55/SNR_G55_10s.tar.gz] <font color=green>(5.0 GB)</font>.  These data are already in the CASA Measurement Set (MS) format and were prepared specifically for this guide. 

The following explains how the data were processed to achieve the above MS file, as it has implications for later flagging steps. 

Note that commands with a grey background do not need to be run in CASA.

The data were first loaded from the [http://data.nrao.edu NRAO archive]. On the archive search form, we specified '''Archive File ID''' to be ''AB1345_sb1800808_1.55431.004049953706'' and selected '''SDM-BDF dataset (all files)''' as the data download option on the following page. Be aware that the full dataset is 170GB!

Once the SDM-BDF was downloaded, we created an MS with the task [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.data.importasdm.html importasdm]:

     ''importasdm(asdm='AB1345_sb1800808_1.55431.004049953706', vis='SNR_G55.ms', process_flags=True, tbuff=1.5, applyflags=False, 
                ocorr_mode='co', savecmds=True, outfile='SNR_G55.ms.onlineflags.txt', flagbackup=False)''

    process_flags=True: This parameter controls the creation of online flags from the Flag.xml SDM table.
                        It will create online flags in the FLAG_CMD sub-table within the MS (more on this later).<br />
             tbuff=1.5: This parameter adds a time buffer padding to the flags in both directions to deal with timing mismatches.
                        This is important for VLA data taken before April 2011. This value should be set to 1.5x integration time.
                        This particular observing session had 1 second correlator integration time.<br />
      applyflags=False: We will apply these flags later in the tutorial.<br />
      ocorr_mode ='co': Only choosing to import the cross-only (co) correlations.<br />
         savecmds=True: Save the online-flag commands to an ASCII file.<br />
    outfile='SNR_G55.ms.onlineflags.txt': This will create a text file with a list of online flags that can be applied to the data.
                                          The online flags within the file will include the time buffer requested in the ''tbuff'' parameter. 
                                          Mainly created for demonstration purposes.

The data were split from the original MS and time-averaged using the CASA task [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.manipulation.split.html split]. 

      ''split(vis='SNR_G55.ms', outputvis='SNR_G55_10s.ms', field='3~5', spw='4~5,7~8', timebin='10s', 
             antenna='!ea06,ea17,ea20,ea26', datacolumn='data', keepflags=False)''

      field='3~5': We only include the complex gain calibrator, flux density scale/bandpass calibrator, and the target source at this stage.<br />
    spw='4~5,7~8': Several spectral windows have been removed which were heavily impacted with RFI, which neither auto-flagging nor
                   hand flagging could remedy. We are keeping spectral windows 4,5,7,8.<br />
    timebin='10s': Time-averaged to 10-seconds, to reduce size and processing time when running tasks. <br />
    antenna='!ea06,ea17,ea20,ea26': Several antennas have been removed, which at the time of the observations, did not have an L-Band
                                    receiver installed (please see the [[#Identifying_Problematic_Antennas_from_the_Operator_Logs | Identifying Problematic Antennas from the Operator Logs]] section).
                                    The exclamation point (!) before ea06 is called a negation operator. It will exclude all the antennas
                                    provided here, as long as they are separated by commas. For more on CASA syntax, please see this page
                                    on [https://casadocs.readthedocs.io/en/v6.2.0/notebooks/visibility_data_selection.html visibility data selection].

== Unpacking the Data == 

Once you've downloaded the MS file from the link above, unzip and untar the file from a terminal window (before starting CASA):

<source lang="bash">
tar -xzvf SNR_G55_10s.tar.gz
</source>

This will create a directory called "SNR_G55_10s.ms" <font color=green>(5.5GB)</font>, which is the MS.


== Starting CASA ==

Start CASA by typing '''casa''' on a terminal command line.  If you have not used CASA before, some helpful tips are available on the [[Getting Started in CASA]] page.

This guide has been written for CASA version 6.4.1.  Please confirm your version before proceeding by checking the message in the command line interface window or the CASA logger after startup.

For this tutorial, we will be running tasks using the ''task (parameter = value)'' syntax. All parameters not explicitly called by this manner will use their default values.
</div>

== Preliminary Data Evaluation == 

As a first step, use [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.information.listobs.html listobs] to have a look at the MS:

<source lang="python">
# In CASA
listobs(vis='SNR_G55_10s.ms', listfile='SNR_G55_10s.listobs')
</source>

*listfile: Creates a text document ''SNR_G55_10s.listobs'' with the summary of the data set. 

The ''SNR_G55_10s.listobs'' text document can be opened with your favorite text viewer.
<pre style="white-space: pre-wrap;">
================================================================================
           MeasurementSet Name:  /lustre/aoc/sciops/akapinsk/CASAguides-6.2.0/flagging/SNR_G55_10s.ms      MS Version 2
================================================================================
   Observer: Dr. Sanjay Sanjay Bhatnagar     Project: uid://evla/pdb/1072564  
Observation: EVLA
Data records: 2732400      Total elapsed time = 26926 seconds
   Observed from   23-Aug-2010/00:56:36.0   to   23-Aug-2010/08:25:22.0 (UTC)

   ObservationID = 0         ArrayID = 0
  Date        Timerange (UTC)          Scan  FldId FieldName          nRows     SpwIds   Average Interval(s)    ScanIntent
  23-Aug-2010/00:56:36.0 - 00:58:06.0    14      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              00:58:06.0 - 00:59:36.0    15      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              00:59:36.0 - 01:01:05.0    16      0 J1925+2106         9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [CALIBRATE_PHASE#UNSPECIFIED]
              01:01:05.0 - 01:02:35.0    17      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              01:02:35.0 - 01:04:05.0    18      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              01:04:05.0 - 01:05:34.0    19      0 J1925+2106         9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [CALIBRATE_PHASE#UNSPECIFIED]
              01:05:34.0 - 01:07:04.0    20      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              01:07:04.0 - 01:08:34.0    21      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:08:34.0 - 01:10:04.0    22      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:10:04.0 - 01:11:34.0    23      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:11:34.0 - 01:13:03.0    24      1 G55.7+3.4          9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [OBSERVE_TARGET#UNSPECIFIED]
              01:13:03.0 - 01:14:33.0    25      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:14:33.0 - 01:16:03.0    26      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:16:03.0 - 01:17:33.0    27      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:17:33.0 - 01:19:02.0    28      1 G55.7+3.4          9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [OBSERVE_TARGET#UNSPECIFIED]
              01:19:02.0 - 01:20:32.0    29      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:20:32.0 - 01:22:02.0    30      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:22:02.0 - 01:23:32.0    31      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:23:32.0 - 01:25:01.0    32      1 G55.7+3.4          9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [OBSERVE_TARGET#UNSPECIFIED]
              01:25:01.0 - 01:26:31.0    33      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:26:31.0 - 01:28:01.0    34      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:28:01.0 - 01:29:31.0    35      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:29:31.0 - 01:31:00.0    36      1 G55.7+3.4          9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [OBSERVE_TARGET#UNSPECIFIED]
              01:31:00.0 - 01:32:30.0    37      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:32:30.0 - 01:34:00.0    38      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:34:00.0 - 01:35:30.0    39      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              01:35:30.0 - 01:36:59.0    40      1 G55.7+3.4          9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [OBSERVE_TARGET#UNSPECIFIED]
              01:36:59.0 - 01:38:29.0    41      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              01:38:29.0 - 01:39:59.0    42      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              01:39:59.0 - 01:41:29.0    43      0 J1925+2106         9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_PHASE#UNSPECIFIED]
              01:41:29.0 - 01:42:58.0    44      1 G55.7+3.4          9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [OBSERVE_TARGET#UNSPECIFIED]
[....]
              08:11:54.0 - 08:13:24.0   305      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              08:13:24.0 - 08:14:54.0   306      1 G55.7+3.4          9108  [0,1,2,3]  [10, 10, 10, 10] [OBSERVE_TARGET#UNSPECIFIED]
              08:14:54.0 - 08:16:24.0   307      2 0542+498=3C147     9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
              08:16:24.0 - 08:17:54.0   308      2 0542+498=3C147     9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
              08:17:54.0 - 08:19:23.0   309      2 0542+498=3C147     9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
              08:19:23.0 - 08:20:53.0   310      2 0542+498=3C147     9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
              08:20:53.0 - 08:22:23.0   311      2 0542+498=3C147     9108  [0,1,2,3]  [10, 10, 10, 10] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
              08:22:23.0 - 08:23:52.0   312      2 0542+498=3C147     9108  [0,1,2,3]  [9.89, 9.89, 9.89, 9.89] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
              08:23:52.0 - 08:25:22.0   313      2 0542+498=3C147     9108  [0,1,2,3]  [10,10,10,10] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_BANDPASS]
           (nRows = Total number of rows per scan) 
Fields: 3
  ID   Code Name                RA               Decl           Epoch   SrcId      nRows
  0    D    J1925+2106          19:25:59.605371 +21.06.26.16218 J2000   0         391644
  1    NONE G55.7+3.4           19:21:40.000000 +21.45.00.00000 J2000   1        2277000
  2    N    0542+498=3C147      05:42:36.137916 +49.51.07.23356 J2000   2          63756
Spectral Windows:  (4 unique spectral windows and 1 unique polarization setups)
  SpwID  Name      #Chans   Frame   Ch0(MHz)  ChanWid(kHz)  TotBW(kHz) CtrFreq(MHz) BBC Num  Corrs          
  0      Subband:0     64   TOPO    1256.000      2000.000    128000.0   1319.0000        4  RR  RL  LR  LL
  1      Subband:2     64   TOPO    1384.000      2000.000    128000.0   1447.0000        4  RR  RL  LR  LL
  2      Subband:1     64   TOPO    1648.000      2000.000    128000.0   1711.0000        8  RR  RL  LR  LL
  3      Subband:0     64   TOPO    1776.000      2000.000    128000.0   1839.0000        8  RR  RL  LR  LL
Sources: 12
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
  0    J1925+2106          0     -              -            
  0    J1925+2106          1     -              -            
  0    J1925+2106          2     -              -            
  0    J1925+2106          3     -              -            
  1    G55.7+3.4           0     -              -            
  1    G55.7+3.4           1     -              -            
  1    G55.7+3.4           2     -              -            
  1    G55.7+3.4           3     -              -            
  2    0542+498=3C147      0     -              -            
  2    0542+498=3C147      1     -              -            
  2    0542+498=3C147      2     -              -            
  2    0542+498=3C147      3     -              -            
Antennas: 23:
  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
                                                                     East         North     Elevation               x               y               z
  0    ea01  W09       25.0 m   -107.37.25.2  +33.53.51.0       -521.9416     -332.7766       -1.2001 -1601710.017000 -5042006.925200  3554602.355600
  1    ea02  E02       25.0 m   -107.37.04.4  +33.54.01.1          9.8240      -20.4293       -2.7806 -1601150.060300 -5042000.619800  3554860.729400
  2    ea03  E09       25.0 m   -107.36.45.1  +33.53.53.6        506.0564     -251.8670       -3.5825 -1600715.950800 -5042273.187000  3554668.184500
  3    ea04  W01       25.0 m   -107.37.05.9  +33.54.00.5        -27.3562      -41.3030       -2.7418 -1601189.030140 -5042000.493300  3554843.425700
  4    ea05  W08       25.0 m   -107.37.21.6  +33.53.53.0       -432.1167     -272.1478       -1.5054 -1601614.091000 -5042001.652900  3554652.509300
  5    ea07  E05       25.0 m   -107.36.58.4  +33.53.58.8        164.9788      -92.8032       -2.5268 -1601014.462000 -5042086.252000  3554800.799800
  6    ea08  N01       25.0 m   -107.37.06.0  +33.54.01.8        -30.8810       -1.4664       -2.8597 -1601185.634945 -5041978.156586  3554876.424700
  7    ea09  E06       25.0 m   -107.36.55.6  +33.53.57.7        236.9058     -126.3369       -2.4443 -1600951.588000 -5042125.911000  3554773.012300
  8    ea10  N03       25.0 m   -107.37.06.3  +33.54.04.8        -39.0773       93.0192       -3.3330 -1601177.376760 -5041925.073200  3554954.584100
  9    ea11  E04       25.0 m   -107.37.00.8  +33.53.59.7        102.8054      -63.7682       -2.6414 -1601068.790300 -5042051.910200  3554824.835300
  10   ea12  E08       25.0 m   -107.36.48.9  +33.53.55.1        407.8285     -206.0065       -3.2272 -1600801.926000 -5042219.366500  3554706.448200
  11   ea13  N07       25.0 m   -107.37.07.2  +33.54.12.9        -61.1037      344.2331       -4.6138 -1601155.635800 -5041783.843800  3555162.374100
  12   ea15  W06       25.0 m   -107.37.15.6  +33.53.56.4       -275.8288     -166.7451       -2.0590 -1601447.198000 -5041992.502500  3554739.687600
  13   ea16  W02       25.0 m   -107.37.07.5  +33.54.00.9        -67.9687      -26.5614       -2.7175 -1601225.255200 -5041980.383590  3554855.675000
  14   ea18  N09       25.0 m   -107.37.07.8  +33.54.19.0        -77.4346      530.6273       -5.5859 -1601139.485100 -5041679.036800  3555316.533200
  15   ea19  W04       25.0 m   -107.37.10.8  +33.53.59.1       -152.8599      -83.8054       -2.4614 -1601315.893000 -5041985.320170  3554808.304600
  16   ea21  E01       25.0 m   -107.37.05.7  +33.53.59.2        -23.8638      -81.1510       -2.5851 -1601192.467800 -5042022.856800  3554810.438800
  17   ea22  N04       25.0 m   -107.37.06.5  +33.54.06.1        -42.6239      132.8436       -3.5494 -1601173.979400 -5041902.657700  3554987.517500
  18   ea23  E07       25.0 m   -107.36.52.4  +33.53.56.5        318.0509     -164.1850       -2.6957 -1600880.571400 -5042170.388000  3554741.457400
  19   ea24  W05       25.0 m   -107.37.13.0  +33.53.57.8       -210.0959     -122.3887       -2.2577 -1601377.009500 -5041988.665500  3554776.393400
  20   ea25  N02       25.0 m   -107.37.06.2  +33.54.03.5        -35.6245       53.1806       -3.1345 -1601180.861480 -5041947.453400  3554921.628700
  21   ea27  E03       25.0 m   -107.37.02.8  +33.54.00.5         50.6641      -39.4835       -2.7273 -1601114.365500 -5042023.151800  3554844.944000
  22   ea28  N08       25.0 m   -107.37.07.5  +33.54.15.8        -68.9057      433.1889       -5.0602 -1601147.940400 -5041733.837000  3555235.956000
</pre>

<div style="text-align: justify;">
* J1925+2106,     field ID 0: The complex gain (amplitude and phase) calibrator;
* G55.7+3.4,      field ID 1: The supernova remnant;
* 0542+498=3C147, field ID 2: The flux density scale/bandpass calibrator.
[[Image:plotAnts.png|300px|thumb|right|'''Figure 1''' <br />Antenna plot showing the configuration during the observing session.]]

We can also see that these sources have associated scan intents that indicate their function in the observations.  Note that you can select sources based on their intents in certain CASA tasks.  The various scan intents in this data set are:

* CALIBRATE_PHASE indicates that this is a scan to be used for complex gain (amplitude and phase) calibration;
* OBSERVE_TARGET indicates that this is the science target;
* CALIBRATE_AMPLI indicates that this is to be used for flux density scale calibration, and; 
* CALIBRATE_BANDPASS indicates that these scans are to be used for bandpass calibration.

Note that more recent data sets use a different naming convention for scan intents (e.g. CALIBRATE_PHASE -> CALIBRATE_AMPLI,CALIBRATE_PHASE and CALIBRATE_AMPLI -> CALIBRATE_FLUX).
<!-- Also note that 3C147 is used for both flux density scale and bandpass calibration.-->

It's important to be aware that the antennas have both a name and an ID associated with them. For example antenna ID 15 is named ea19 (the ''ea'' stemming from the Expanded VLA project). When specifying an antenna within a task parameter, we will primarily reference them by their ''ea'' name. 

We can see the antenna configuration for this observing session by using [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.visualization.plotants.html plotants]. 

<source lang="python">
# In CASA
plotants(vis='SNR_G55_10s.ms', figfile='SNR_G55_10s.plotants.png')
</source>

Figure 1 the antenna configuration for our observations; antennas ea01, ea03, and ea18 were on the extreme ends of the west, east, and north arms, respectively.  

<!-- This is really not for this guide, so commented out for the time being. ADK, Oct 2018-->
<!-- The antenna position diagram is particularly useful as a guide to help determine which antenna to use as the reference antenna later during calibration. Antennas on station 8 of each arm (N08, E08, W08) do not get moved during array re-configurations; they can, therefore, at times be good choices as reference antennas. In this case, we'll probably want to choose something closer to the center of the array with no shadowing.-->


=== Identifying RFI with Plotms() ===
[[Image:CASA5.4.0-FLAG-Plotms-amp-time.png|300px|thumb|right|'''Figure 2''' <br />Plotms image of supernova remnant data, showing strong RFI through the observation (x axis) and affecting a number of spectral windows (data are colorised by spw).]]

The data can be inspected with the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms] task. 

It is worth first having a look at the data, separately per each field, in <b>amplitude vs. frequency</b> (to identify narrow-band RFI) and <b>amplitude vs. time</b> (intermittent RFI). 

To start with, let's look at the supernova remnant observations (field='1') for all scans (default) and all antennas (default):

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s.ms', field='1', xaxis='time', yaxis='amp', coloraxis='spw')
</source>

We can immediately see that there is plenty of RFI throughout the observations, affecting a number of spectral windows (data are colorised by spectral window; Figure 2). The RFI is discerned by the large spikes in amplitude.

To narrow down where the RFI occurs let's now have a look at the data in amplitude vs frequency, plotted separately per each scan:

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s.ms', scan='30,75,120,165,190,235,303', antenna='ea24', xaxis='freq', 
       yaxis='amp', coloraxis='spw', iteraxis='scan')
</source>
[[Image:amp_v_freq_rawdata.png|300px|thumb|right|'''Figure 3''' <br />Plotms image of scan 190 showing strong RFI spikes in amplitude for several spectral windows.]]
* coloraxis='spw': Parameter indicates that a different color will be assigned to each spectral window.
* antenna='ea24' : Here we chose only information for antenna ea24.
* iteraxis='scan': Parameter tells plotms to iterate over scans, that is to display a new plot for each scan. 

The command above will set the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms] for iteration, but if you want to set this option from within [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms], go onto the Plot tab (horizontal), and then Page tab (vertical). You will now find Iteration options. Set Axis to the parameter you want to iterate through. Iterate by clicking on the green arrow buttons on the toolbar within the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms]. 

Progressing through to scan 190 , we can see there is significant time and frequency variable RFI present in the observing session. To determine which spectral windows are affected, click on the <b>Mark Regions</b> tool at the bottom of the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms] GUI (the open box with a green plus sign) and use the mouse to select a few of the highest-amplitude points in each of the spectral windows (Figure 3). Click on the <b>Locate</b> button (magnifying glass on white background). Information about the selected areas should now display in the logger window. For example:
<br />
</div>
<pre>
 INFO PlotMS Frequency in [1.30517 1.31368] or [1.32584 1.33313] or [1.68146 1.69544], Amp in [0.132051 0.223077] or [0.124359 0.188034] or [0.139316 0.237179]:
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea01@W09 & ea24@W05[0&19]  Spw=0 Chan=27 Freq=1.31 Corr=LR X=1.31 Y=0.139029 (110/144/110)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea03@E09 & ea24@W05[2&19]  Spw=0 Chan=27 Freq=1.31 Corr=LL X=1.31 Y=0.145391 (623/144/623)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea04@W01 & ea24@W05[3&19]  Spw=0 Chan=27 Freq=1.31 Corr=LL X=1.31 Y=0.166033 (879/144/879)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea04@W01 & ea24@W05[3&19]  Spw=0 Chan=37 Freq=1.33 Corr=LR X=1.33 Y=0.131179 (918/144/918)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea07@E05 & ea24@W05[5&19]  Spw=0 Chan=27 Freq=1.31 Corr=RL X=1.31 Y=0.14596  (1389/144/1389)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea07@E05 & ea24@W05[5&19]  Spw=0 Chan=27 Freq=1.31 Corr=LL X=1.31 Y=0.142578 (1391/144/1391)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea09@E06 & ea24@W05[7&19]  Spw=0 Chan=27 Freq=1.31 Corr=RR X=1.31 Y=0.141398 (1900/144/1900)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea12@E08 & ea24@W05[10&19] Spw=0 Chan=37 Freq=1.33 Corr=LR X=1.33 Y=0.133163 (2710/144/2710)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea13@N07 & ea24@W05[11&19] Spw=0 Chan=37 Freq=1.33 Corr=RR X=1.33 Y=0.129079 (2964/144/2964)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea15@W06 & ea24@W05[12&19] Spw=0 Chan=27 Freq=1.31 Corr=RR X=1.31 Y=0.135901 (3180/144/3180)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea16@W02 & ea24@W05[13&19] Spw=0 Chan=27 Freq=1.31 Corr=RR X=1.31 Y=0.17187  (3436/144/3436)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea16@W02 & ea24@W05[13&19] Spw=0 Chan=27 Freq=1.31 Corr=LR X=1.31 Y=0.155113 (3438/144/3438)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea16@W02 & ea24@W05[13&19] Spw=0 Chan=27 Freq=1.31 Corr=LL X=1.31 Y=0.142598 (3439/144/3439)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea19@W04 & ea24@W05[15&19] Spw=0 Chan=27 Freq=1.31 Corr=LR X=1.31 Y=0.154241 (3950/144/3950)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea19@W04 & ea24@W05[15&19] Spw=0 Chan=27 Freq=1.31 Corr=LL X=1.31 Y=0.178607 (3951/144/3951)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea19@W04 & ea24@W05[15&19] Spw=0 Chan=37 Freq=1.33 Corr=RR X=1.33 Y=0.126879 (3988/144/3988)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea21@E01 & ea24@W05[16&19] Spw=0 Chan=27 Freq=1.31 Corr=RL X=1.31 Y=0.144868 (4205/144/4205)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea21@E01 & ea24@W05[16&19] Spw=0 Chan=27 Freq=1.31 Corr=LL X=1.31 Y=0.158044 (4207/144/4207)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:19:58.0 BL=ea22@N04 & ea24@W05[17&19] Spw=0 Chan=37 Freq=1.33 Corr=RR X=1.33 Y=0.18105  (4500/144/4500)
<snip>
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:08.0 BL=ea22@N04 & ea24@W05[17&19] Spw=2 Chan=19 Freq=1.686 Corr=RR X=1.686 Y=0.195303(10060/169/4428)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:08.0 BL=ea22@N04 & ea24@W05[17&19] Spw=2 Chan=19 Freq=1.686 Corr=RL X=1.686 Y=0.19185 (10061/169/4429)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:08.0 BL=ea22@N04 & ea24@W05[17&19] Spw=2 Chan=21 Freq=1.69 Corr=RR X=1.69 Y=0.169598  (10068/169/4436)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea08@N01 & ea24@W05[6&19]  Spw=2 Chan=19 Freq=1.686 Corr=LR X=1.686 Y=0.157531(7246/170/1614)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea10@N03 & ea24@W05[8&19]  Spw=2 Chan=19 Freq=1.686 Corr=LL X=1.686 Y=0.15168 (7759/170/2127)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea15@W06 & ea24@W05[12&19] Spw=2 Chan=19 Freq=1.686 Corr=LR X=1.686 Y=0.202071(8782/170/3150)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea18@N09 & ea24@W05[14&19] Spw=2 Chan=21 Freq=1.69 Corr=RR X=1.69 Y=0.159526  (9300/170/3668)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea19@W04 & ea24@W05[15&19] Spw=2 Chan=19 Freq=1.686 Corr=RR X=1.686 Y=0.192973(9548/170/3916)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea19@W04 & ea24@W05[15&19] Spw=2 Chan=19 Freq=1.686 Corr=LR X=1.686 Y=0.155768(9550/170/3918)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea19@W04 & ea24@W05[15&19] Spw=2 Chan=19 Freq=1.686 Corr=LL X=1.686 Y=0.147995(9551/170/3919)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea22@N04 & ea24@W05[17&19] Spw=2 Chan=19 Freq=1.686 Corr=RR X=1.686 Y=0.199225(10060/170/4428)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea22@N04 & ea24@W05[17&19] Spw=2 Chan=19 Freq=1.686 Corr=RL X=1.686 Y=0.193489(10061/170/4429)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea22@N04 & ea24@W05[17&19] Spw=2 Chan=21 Freq=1.69 Corr=RR X=1.69 Y=0.179036  (10068/170/4436)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea24@W05 & ea25@N02[19&20] Spw=2 Chan=19 Freq=1.686 Corr=RL X=1.686 Y=0.156535(10573/170/4941)
 INFO PlotMS Scan=190 Field=G55.7+3.4[1] Time=2010/08/23/05:21:17.5 BL=ea24@W05 & ea25@N02[19&20] Spw=2 Chan=21 Freq=1.69 Corr=RR X=1.69 Y=0.140293  (10580/170/4948)
 INFO PlotMS Found 287 points (287 unflagged) among 202752 in 0.01s.
</pre>
<div style="text-align: justify;">

{|style="margin: 0 auto;"
| [[Image:RFI_1244-1372.png|380px|thumb|right|'''Figure 4a''' <br />Amplitude vs. frequency plot of a portion of the L-band spectrum, showing RFI spikes from different sources.]]
| [[Image:amp_v_freq.spw0_Scan190.png|330px|thumb|right|'''Figure 4b''' <br />Amplitude vs. frequency plot of L-Band, spectral window 0, for scan 190. Generated by running the command "plotms(vis='SNR_G55_10s.ms', spw='0', scan='190', xaxis='freq', yaxis='amp')" within CASA.]]
|}

Reviewing the log output, we  see that spw 0 and 2 are affected the most by RFI. We also get the corresponding frequency where the RFI is present, which appears to be 1.31 and 1.33 GHz for spectral window 0, and 1.686 GHz for spectral window 2. This information is important, especially when flagging data interactively as we will be doing towards the end of this guide.

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s.ms', spw='0', scan='190', xaxis='freq',yaxis='amp')
</source>

The VLA has obtained RFI sweeps over its full frequency range. The results are available on the [https://science.nrao.edu/facilities/vla/docs/manuals/obsguide/modes/rfi Radio Frequency Interference website.] Most of the RFI features can be identified as radar, communications, satellites, airplanes, or birdies (i.e., RFI generated by the VLA electronics itself). For our observations, we inspect the L-band specific RFI plots [https://science.nrao.edu/facilities/vla/observing/RFI/L-Band website] and find that the 1310 and 1330 MHz features are due to FAA ASR radars, while the one at 1686 MHz is most likely due to a GOES weather satellite. We can compare the plots of the FAA ASR radar from the website (Figure 4a), with that of spw 0 (Figure 4b), and see that the spikes are practically identical and fall within the same frequencies.


== Identifying Problematic Antennas from the Operator Logs ==

We first check the operator log for the observing session to see if there were any issues noted during the run that need to be addressed. The logs are available from the [http://www.vla.nrao.edu/cgi-bin/oplogs.cgi VLA operator log website]. Here is the link for the [http://www.vla.nrao.edu/operators/logs/2010/8/2010-08-23_0005_AB1345.pdf observing log] file for our observing session.

The log has various pieces of information including the start/end times for the observing session, frequency bands used, weather, baseline information for recently moved antennas, and any outages or issues that may have been encountered. We see that antenna ea07 may need position corrections (see one of our calibration tutorials, [https://casaguides.nrao.edu/index.php?title=VLA_high_frequency_Spectral_Line_tutorial_-_IRC%2B10216-CASA6.4.1  IRC+10216], on how to fix this), and several antennas (ea06, ea17, ea20, and ea26) are missing an L-Band receiver. Antenna 07 position corrections will need to be applied during data calibration and will not be covered in this tutorial. Additionally, the antennas with missing receivers were already removed from the dataset used here (as explained in the above section Obtaining the Data), so we can continue with online flagging.
<br />
<br />

== Online Flags ==

At the time of importing from the SDM-BDF raw data to a MS, we chose to process the online flags from the Flags.xml file to the FLAG_CMD sub-table within the MS. We also created the ''SNR_G55.ms.onlineflags.txt'' file, a plain text document that includes the list of online flags. Note that this step is not necessary if you choose to apply online flags at the time of the data download from the archive.

The Flags.xml file holds information of flags created during the observing session, such as subreflector issues and antennas not being on source. 
We will now apply these online flags to the data by employing [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagcmd.html flagcmd], but first, let's create a plot of the flags to get an idea of what will be flagged.

[[Image:OnlineFlags_CASA6.2.0.png|300px|thumb|right|'''Figure 5''' Online Flags]]

<source lang="python">
# In CASA
flagcmd(vis='SNR_G55_10s.ms', inpmode='table', reason='any', action='plot', plotfile='flaggingreason_vs_time.png')
</source>

Open the ''flaggingreason_vs_time.png'' with your favorite image viewing program. Figure 5 shows several instances of online flagging. Most notably, ea28 and ea08 had some subreflector issues throughout the observing session. Online flags are instances of possible missing data, including:

* ANTENNA_NOT_ON_SOURCE 
The VLA antennas have slewing speeds of 40 degrees per minute in azimuth and 20 degrees per minute in elevation. Some antennas are slower than others and may take a few more seconds to reach the next source. The antennas can also take a few seconds to settle down due to small oscillations after having slewed. 

* SUBREFLECTOR_ERROR    
The Focus Rotation Mount (FRM), located at the apex of the antenna, is responsible for focusing the incoming radio signal to the corresponding receiver. At times there can be issues with the focus and/or rotation axes.

Now that we've plotted the online flags, we will apply them to the MS. 

<source lang="python">
# In CASA
flagcmd(vis='SNR_G55_10s.ms', inpmode='table', reason='any', action='apply', flagbackup=False)
</source>

* inpmode='table': Will use the online-flags imported to the FLAG_CMD sub-table from the Flags.xml file. This was done during the importing of our data with [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.data.importasdm.html importasdm]. Note that the FLAG_CMD sub-table already includes a 1.5 second time buffer, as was requested during the importing of the data (parameter ''tbuff=1.5'').

The CASA logger should report the progress as the task applies these flags in segments. Once finished, it will report the percentage of flagged data. The terminal window will  display warnings about the four missing antennas; this is expected as we had previously removed the antennas during the split task.

Alternatively, we could have applied the online flags from the text file (''SNR_G55.ms.onlineflags.txt'') created during the importing of the data. The one caveat when it comes to applying flags from a list is not being able to un-apply them (setting parameter ''action='unapply' ''within [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagcmd.html flagcmd]. Transferring the flags to the FLAGS_CMD table ''before'' applying them ''does'' allow for the use of the un-apply feature. For convenience, we provide the command for applying online flags from a list (don't run the following command in CASA):

<pre>
flagcmd(vis='SNR_G55_10s.ms', inpmode='list', inpfile='SNR_G55.ms.onlineflags.txt', reason='any', action='apply', flagbackup=False)
</pre>

== Shadowed Antennas ==

The VLA D-configuration is the most compact; there may be instances where one antenna blocks, or shadows another. For more on shadowing, please refer to the [https://science.nrao.edu/facilities/vla/docs/manuals/obsguide/dynsched#section-1 antenna shadowing] section in the [https://science.nrao.edu/facilities/vla/docs/manuals/obsguide Guide to Observing with the VLA]. Generally, observing sources at 40 degrees elevation and higher will result in less shadowing. We will create a plot of elevation vs. time by using the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms] task and note the elevation of the radio sources we observed.

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s.ms', xaxis='time', yaxis='elevation', antenna='0&1;2&3', spw='*:31',
       coloraxis='field', title='Elevation vs. Time', plotfile='Elevation_vs_Time.png')
</source>

[[Image:Elevation_vs_Time.png|300px|thumb|right|'''Figure 6''' Plot of elevation vs. time.]]

Figure 6 shows that most of the sources were at or above 40 degrees in elevation; accordingly, we expect a minimal amount of shadowing. The flux density scale/ bandpass calibrator 3C147 was observed towards the end of the session, which could result in some shadowing of antennas due to its low elevation of about 20&ndash;22 degrees. 

Task [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] can determine and flag shadowed antennas by their location and observing direction:

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s.ms', mode='shadow', tolerance=0.0, flagbackup=False)
</source>
* ''mode='shadow''': has a subparameter ''tolerance=0.0'' that controls how many meters of shadowing overlap is allowed

The logger will report on the percentage of flagged data due to shadowing. As expected in this observing session, there does not appear to be much data affected by shadowing (approx. 0.4%).

== Zero-Amplitude Data ==

In addition to shadowing, there may be times during which the correlator writes out pure zero-valued data.  In order to remove this bad data, we run [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] to remove any pure zeroes:

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s.ms', mode='clip', clipzeros=True, flagbackup=False) 
</source>
* ''mode='clip''': is used to flag all values below a given threshold. With ''clipzeros=True'' this mode will flag exact zero values that are sometimes being produced by the VLA correlator.

Inspecting the logger output generated by [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] shows that there is a small quantity of zero-valued data present in this MS.

== Quacking ==

Now we utilize the flagdata task one more time to run quacking mode.

It's common for the array to settle down at the start of a scan. Quacking is used to remove data at scan boundaries, the same edit can be applied to all scans for all baselines. 
 
<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s.ms', mode='quack', quackinterval=5.0, quackmode='beg', flagbackup=False)
</source>

*quackmode='beg': Data from the start of each scan will be flagged.
*quackinterval=5.0: Flag the first 5 seconds of every scan.


== Backup Data - Flagmanager ==

Flags can be backed up in a file ''ms.flagversions'' that is related to the MS. For our MS, the related flag backups are stored in ''SNR_G55_10s.ms.flagversions''. 

'''Note: flags that are applied to the data are contained in the MS;''' '''''ms.flagversions''''' '''only contains backup flags that can be restored if required.'''

Most flagging tasks, like [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata], offer a ''flagbackup'' parameter that controls whether or not the current flags are being backed up in ms.flagversions before new (additional) flags will be applied. Backup flags can also be manually saved to or restored from ms.flagversions using the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagmanager.html flagmanager] task.   

Now that we've applied online flags, clipped zero amplitude data, removed shadowed data, and quacked the data, we will create a backup of the flags by setting the parameter ''versionname='after_online_flagging' '': 

<source lang="python">
# In CASA
flagmanager(vis='SNR_G55_10s.ms', mode='save', versionname='after_online_flagging')
</source>

The version we just created is saved inside the SNR_G55_10s.ms.flagversions directory. From here onward, if we make a mistake, we can always revert back to this flag version of the MS by setting parameter ''mode='restore' '' and providing the version name we want to revert back to, such as:

<pre>
flagmanager(vis='SNR_G55_10s.ms', mode='restore', versionname='after_online_flagging')
</pre>

The flagmanager() can also be run on calibration tables. In this instance just specify the table name as the ''vis'' parameter and run is as above.

== Benefit of Hanning Smoothing ==

Strong RFI sources can give rise to the Gibbs phenomenon. This is seen by ringing: a zig-zag pattern across the channels that neighbor the strong, usually narrow, RFI. To remedy this ringing across the frequency channels, we employ the Hanningsmooth algorithm via the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.manipulation.hanningsmooth.html hanningsmooth] task (an implementation based on [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.manipulation.mstransform.html mstransform]). Hanning-smoothing applies a triangle kernel across the pattern which diminishes the ringing, reducing the number of channels that may look bad and get flagged. Note that this smoothing procedure will also decrease the spectral resolution by a factor of two.

The task requires the creation of a new MS, which we will call ''SNR_G55_10s-hanning.ms''. 

<b>Note: As Hanning-smoothing will remove amplitude spikes, it is not recommended for spectral analysis related science (e.g. strong narrow maser lines).</b>

Let's create before (Figure 7a) and after images (Figure 7b) with the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms] task to see the effect. 

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s.ms', scan='190', antenna='ea24', spw='0~2',
       xaxis='freq', yaxis='amp', coloraxis='spw', title='Before Hanning',
       correlation='RR,LL', plotrange=[1.2,1.8,-0.01,0.25],
       plotfile='amp_v_freq.beforeHanning.png')
</source><br />

<source lang="python">
# In CASA
hanningsmooth(vis='SNR_G55_10s.ms', outputvis='SNR_G55_10s-hanning.ms', datacolumn='data')
</source><br />

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='190', antenna='ea24', spw='0~2',
       xaxis='freq', yaxis='amp', coloraxis='spw', title='After Hanning',
       correlation='RR,LL', plotrange=[1.2,1.8,-0.01,0.25],
       plotfile='amp_v_freq.afterHanning.png')
</source>

{|style="margin: 0 auto;"
| [[Image:amp_v_freq.beforeHanning.png|350px|thumb|right|'''Figure 7a''' <br />Plot of amplitude vs. frequency before Hanning smoothing data.]]
| [[Image:amp_v_freq.afterHanning.png|350px|thumb|right|'''Figure 7b''' <br />Plot of amplitude vs. frequency after Hanning smoothing data.]]
|}

Figure 7b shows the effect of applying Hanning-smoothing. Notice that single channel RFI has spread into three channels. This spreading of RFI to other channels will ultimately result in a little more data being flagged.

== Automatic RFI Excision ==

Now that we're done with online flagging, we can move on to removing some of the RFI present with auto-flagging algorithms used within [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata], TFCrop and rflag. For further details on the two algorithm based tasks we will employ, please see the [https://science.nrao.edu/science/meetings/2016/vla-data-reduction/EVLAWorkshop_RFI_2016_UR.pdf RFI presentation] given at the 5th VLA Data Reduction Workshop.

=== TFCrop ===

Task [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata's] TFCrop is an algorithm that detects outliers in the 2D time-frequency plane and can operate on uncalibrated (non-bandpass corrected) data. TFCrop will iterate through segments of time and undergo several steps in order to find and excise different types of RFI:

Step 1: Detect short-duration RFI spikes (narrow- and broad-band). <br />
Step 2: Search for time-persistent RFI. <br />
Step 3: Search for time-persistent, narrow-band RFI. <br />
Step 4: Search for low-level wings of very strong RFI. <br />

[[Image:amp_v_freq_before_tfcrop.png|350px|thumb|right|'''Figure 8''' <br />Amplitude vs. Frequency plot of Scan 190, before the TFCrop algorithm is applied.]]
We will apply the auto-flagging TFCrop algorithm for each spectral window. With TFCrop, it's a good idea to first inspect a small portion of data and review what and how much will be flagged. Once you are comfortable with the results, you can apply the algorithm to the remaining data. We will walk through the first spw and then include the remaining spws with the same command. First plot the corrected data for scan 190 (Figure 8) with all spectral windows so we can compare the data before and after TFCrop.

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='190', antenna='ea24', xaxis='freq', iteraxis='scan', yaxis='amp',
       ydatacolumn='data', plotfile='amp_v_freq_before_tfcrop.png', title='Before TFCrop',
       coloraxis='spw', plotrange=[1.2,2,-0.01,0.25])
</source>

The following are a set of [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] commands which have been found to work reasonably well with these data. Take some time to play with the parameters, and the plotting capabilities, as this will be important when you are working with your own data later on. Because we set parameters ''display='both' ''and ''action='calculate', '' the flags are displayed but not actually written to the MS. This allows one to try different sets of parameters before actually applying the flags to the data.
[[Image:Tfcrop.png|350px|thumb|right|'''Figure 9''' <br />TFCrop flagging results. Top row is before, and bottom row is after TFCrop has applied flagging.]]

Some representative TFCrop plots are displayed (Figure 9). Each column displays an individual polarization product; all four polarizations are, from left to right, RR, RL, LR, and LL. The first row shows the data with current flags applied and the second includes the flags generated by flagdata. The x-axis is channel number (the spectral window ID is displayed in the top title) and the y-axis of the first two rows is all integrations included in a time segment, set by the parameter ''ntime''. These are the data considered by the TFCrop algorithm during its flagging process, and changes in ''ntime'' will have some (relatively small) effect on what data are flagged. 

Each plot page displays data for a single baseline and time segment, with colours representing the intensity of the visibilities (amplitude) in the heat colour scheme ranging from black for lowest amplitude points to white for highest amplitude data points. The flagged, or to be flagged, visibilities are masked in blue. The buttons at the bottom allow one to step through baseline (backward and forward), spw, scan, and field while Stop Display will continue the flagging operation without the GUI, and Quit aborts the run.

''' spw 0 '''

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='tfcrop', spw='0',
         datacolumn='data', action='calculate',
         display='both', flagbackup=False)
</source>

The first two scans (14,15) are fully flagged (hence displayed as completely blue). Click on Next Scan until you reach scan 17 where it will be easier to see the flagging the algorithm performs. The top row shows current flags already applied to the data. The bottom row illustrates the flagging that can be applied with TFCrop, represented by the additional blue areas. Iterate through several scans and baselines. Once you're done, click on the Quit button on the bottom right corner. Let's now apply these flags by changing the action parameter.

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='tfcrop', spw='0',
         datacolumn='data', action='apply',
         display='', flagbackup=False)
</source>

The logger will report the percentage of flagged data in the table selection. We can now apply the TFCrop algorithm to the remaining spectral windows. 

''' spw 1, 2, 3 '''

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='tfcrop', spw='1~3',
         datacolumn='data', action='apply',
         display='both', flagbackup=False)
</source>
Iterate through several scans and baselines and, once you're ready to apply the flags, click on Stop Display. After TFCrop has gone through and flagged some of the worst RFI, we can inspect the log report and take note of how much has been flagged.

We can also use [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms] to review the effects of using TFCrop. 

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='190', antenna='ea24', xaxis='freq', iteraxis='scan', yaxis='amp',
       ydatacolumn='data', plotfile='amp_v_freq_after_tfcrop.png', title='After TFCrop',
       correlation='RR,LL', coloraxis='spw', plotrange=[1.2,2,-0.01,0.25])
</source>

Compare the plots before applying TFCrop (Figure 8) to the plot after applying TFCrop (Figure 10). Figure 10 shows great improvements, especially for spectral window 0 and 2, which had some of the worst RFI.

{|style="margin: 0 auto;"
| [[Image:amp_v_freq_before_tfcrop.png|350px|thumb|right|'''Figure 8''' <br />Amplitude vs. Frequency plot of Scan 190, before the TFCrop algorithm is applied.]]
| [[Image:amp_v_freq_after_tfcrop_Scan190.png|350px|thumb|right|'''Figure 10''' <br />Plot of amplitude vs. frequency showing the effects of applying TFCrop to our data, for scan 190.]]
|}

''' Flagging Summary '''

We now calculate the amount of data flagged so far in our Measurement Set by using the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] task with parameter ''mode='summary' ''and assign the returned Python dictionary to the variable flagInfo. 

<source lang="python">
# In CASA
flagInfo = flagdata(vis='SNR_G55_10s-hanning.ms', mode='summary')
</source><br />

Now we parse the dictionary to print some of the flagging statistics, first per source, then per spectral windows.

<source lang="python">
# In CASA
print("\n %2.1f%% of G55.7+3.4, %2.1f%% of 3C147, and %2.1f%% of J1925+2106 are flagged. \n" % 
     (100.0 * flagInfo['field']['G55.7+3.4']['flagged'] / flagInfo['field']['G55.7+3.4']['total'], 
     100.0 * flagInfo['field']['0542+498=3C147']['flagged'] / flagInfo['field']['0542+498=3C147']['total'], 
     100.0 * flagInfo['field']['J1925+2106']['flagged'] / flagInfo['field']['J1925+2106']['total']))
</source><br />

Note: IPython currently prevents copy/pasting several lines of code. To remedy this, we will use the %cpaste command to allow multiple lines to be placed in the terminal. Make sure you also copy the "--" characters to close the %cpaste input.

<source lang="python">
# In CASA
%cpaste

# Press Enter or Return, then copy/paste the following:
print("Spectral windows are flagged as follows:")

for spw in range(0,4):
     print("SPW %s: %2.1f%%" % (spw, 100.0 * flagInfo['spw'][str(spw)]['flagged'] / flagInfo['spw'][str(spw)]['total']))
--
</source>

We can now move to the other auto-flagging algorithm, rflag.

=== RFlag ===

RFlag, like TFCrop, is an autoflag algorithm which uses a sliding window statistical filter. Data are iterated through in segments of time where statistics are accumulated and thresholds calculated. 

'''WARNING:''' It is important to not assume that rflag can run on your target. This is especially important for spectral lines, as it may mistake them for interference. 

'''IMPORTANT:''' Task [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata (rflag)] should be executed <u>on calibrated data only</U>. For more details, please see Emmanuel Momjian's presentation on [https://science.nrao.edu/science/meetings/2016/vla-data-reduction/E_Momjian_Data_Reduction_Techniques_Calibration_2016.pdf VLA Data Reduction Techniques and Calibration] given during the [https://science.nrao.edu/science/meetings/2016/vla-data-reduction 5th VLA Data Reduction Workshop].

<div style="background-color: #eeeeee; margin: 40px">
<div style="background-color: #eeeeee; margin: 43px">
<BR>
==== Bandpass calibration (to demonstrate RFlag) ====

For the purpose of demonstrating the functionality of RFlag on our data, we need to perform bandpass calibration first. Here, we just briefly outline the bandpass calibration process. For detailed calibration tutorial see [https://casaguides.nrao.edu/index.php/Karl_G._Jansky_VLA_Tutorials#VLA_Data_Reduction_Tutorials VLA Data Reduction Tutorials].

First, run [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.calibration.gaincal.html gaincal] to solve for an initial set of antenna-based phases over a narrow range of channels. To find channels for each spectral window that are relatively RFI-free over the course of the observing session, look at the data with [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms]. Use only a narrow channel range.
<!-- 
THIS IS NOT NEEDED FOR THIS FLAGGING TUTORIAL, REF TO CALIBRATION TUTORIALS GIVEN

In order to get the best possible result from the automatic RFI excision with {{flagdata}}'s mode ''rflag'', we will first apply bandpass calibration to the MS. Since the RFI is time-variable, using the complex gain calibration source to make an average bandpass over the entire observing session will mitigate the amount of RFI present in the calculated bandpass. For the final calibration, we will use the designated bandpass source 3C147, which will give a much higher signal to noise in the bandpass. Since 3C147 was only observed in the last set of scans, it doesn't sample the time variability and would not provide a good average bandpass.

Since there are likely to be gain variations over the course of the observing session, we will run {{gaincal}} to solve for an initial set of antenna-based phases over a narrow range of channels.  Those solutions will be applied to the data when the bandpass solutions are determined.  While amplitude variations will have little effect on the bandpass solutions, it is important to solve for these phase variations with sufficient time resolution to prevent decorrelation when vector averaging the data in computing the bandpass solutions.

In order to choose a narrow range of channels for each spectral window that are relatively RFI-free over the course of the observing session, we can look at the data with {{plotms}}.  Note that it's important to solve only for phase using a narrow channel range, since an antenna-specific delay will cause the phase to vary with respect to frequency over the spectral window, perhaps by a substantial amount.
-->

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='42,65,88,11,134,157', antenna='ea24', xaxis='channel', 
       yaxis='amp', iteraxis='spw')
</source>

Iterating over each spectral window plot, search for channel ranges with stable amplitudes. An example of a few appropriate channel ranges include: SPW 0:20~24, SPW 1:49~52, SPW 2:38~41, SPW 3:41~44.

Using these ranges, run [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.calibration.gaincal.html gaincal] to calculate phase-only solutions that will be used as input during the initial bandpass calibration. Remember: the calibration tables we are creating now are so that we can use an automatic RFI flagging algorithm. The final calibration tables will be generated later, after automated flagging. Here are the inputs for the initial pre-bandpass phase calibration:

<source lang="python">
# In CASA
gaincal(vis='SNR_G55_10s-hanning.ms', caltable='SNR_G55_10s-hanning.initPh', field='J1925+2106', 
        solint=' int ', spw='0:20~24,1:49~52,2:38~41,3:41~44', refant='ea24', minblperant=3, 
        minsnr=3.0, calmode='p')
</source>
<!--
THIS IS NOT NEEDED FOR THIS FLAGGING TUTORIAL, REF TO CALIBRATION TUTORIALS GIVEN

* caltable='SNR_G55_10s-hanning.initPh': this is the output calibration table that will be written.
* field='J1925+2106': this is the complex gain calibrator we will use for calibration.
* solint=' int ': we request a solution for each 10-second integration.
* spw='0:20~24,1:49~52,2:38~41,3:41~44': note the syntax of this selection: a ''''':''''' is used to separate the SPW from channel selection and '''''~''''' is used to indicate an inclusive range.  
* refant='ea24': we have chosen ea24 as the reference antenna after inspecting the antenna position diagram (see above). It is relatively close to the center of the array. Since the antennas in the very center have a high probability of being shadowed by nearby antennas, choose one that is not directly in the center. This is most important for the more compact (D, C) array configurations.
[[Image:gain.phase_v_time.AllAnt.plotcal.png|300px|thumb|right|'''Figure 7b''' <br /> Gain Phase vs. Time for spw0, for all antennas, with plotsymbol='-', in order to connect the data points and inspect for phase jumps.]]
* minblperant=3: the minimum number of baselines which must be present to attempt a phase solution.
* minsnr=3.0: the minimum signal-to-noise a solution must have to be considered acceptable.  Note that solutions which fail this test will cause these data to be flagged downstream of this calibration step.
* calmode='p': perform phase-only solutions.

Note that a number of solutions do not pass the requirements of the minimum 3 baselines (generating the terminal message''' "Insufficient unflagged antennas to proceed with this solve."''') or minimum signal-to-noise ratio (outputting''' "n of x solutions rejected due to SNR being less than 3 ..."'''). The logger output indicates 320-324 solutions succeeded out of 387 attempted. 
[[Image:gain.phase_v_time.plotcal.png|300px|thumb|right|'''Figure 7a''' <br /> Gain Phase vs. Time for spw0, for four antennas.]]
-->
[[Image:CASA5.4.0-Plotms-pahse-time.png|300px|thumb|right|'''Figure 11''' <br /> Gain Phase vs. Time for spw0, for four antennas.]]

It is always a good idea to inspect the resulting calibration table. We can do this with [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms], which can plot calibration tables as well as visibilities via the "vis" parameter.

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.initPh', xaxis='time', yaxis='phase', 
       iteraxis='spw', antenna='ea01,ea05,ea10,ea24', coloraxis='Antenna1')
</source>


Figure 11 shows the phases do not change much over the course of the observing session. 
<!-- 
THIS IS NOT NEEDED FOR THIS FLAGGING TUTORIAL, REF TO CALIBRATION TUTORIALS GIVEN
We deliberately chose to only plot four antennas in our last call to plotcal, as plotting all of them together will make the plot look convoluted which, in turn, makes it difficult to determine any phase jumps that may be present. To remedy this, we will employ plotcal again with the plotsymbol parameter set to connect the data points.

<source lang="python">
# In CASA
plotcal(caltable='SNR_G55_10s-hanning.initPh', xaxis='time', yaxis='phase', 
        iteration='spw', antenna='', plotsymbol = '-', plotrange=[-1,-1,-180,180])
</source>

Figure 7b may look to have phase jumps, but the V-shapes present are the program attempting to wrap the data points. As a user exercise, plot the phase from -180 to 0, and 0 to +180 to get the stable lines.
-->

Since the plots look fairly reasonable, we will now create a time-averaged bandpass solution for the complex gain calibration source using the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.calibration.bandpass.html bandpass] task.

<source lang="python">
# In CASA
bandpass(vis='SNR_G55_10s-hanning.ms', caltable='SNR_G55_10s-hanning.initBP', 
         field='J1925+2106', solint=' inf ', combine='scan', refant='ea24', 
         minblperant=3, minsnr=10.0, gaintable='SNR_G55_10s-hanning.initPh', 
         interp='nearest', solnorm=False)
</source>
<!--
THIS IS NOT NEEDED FOR THIS FLAGGING TUTORIAL, REF TO CALIBRATION TUTORIALS GIVEN

* solint=' inf ', combine='scan': the solution interval of infinite, up to the boundaries controlled by the combine parameter; this requests that the solution intervals be combined over scans, so that we will get one solution per antenna.
* gaintable= 'SNR_G55_10s-hanning.initPh': we will pre-apply the initial phase solutions.
* interp='nearest': by default, {{bandpass}} will use linear interpolation for pre-applied calibration.  However, we want the <i>nearest</i> phase solution to be used for a given time.

Again, we can see that a number of solutions have been rejected by our choice of <tt>minsnr</tt>.
-->

Now, inspect the resulting bandpass plots with plotms (Figures 12a,b,c). 

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.initBP',xaxis='freq', yaxis='amp', iteraxis='antenna', 
        coloraxis='corr',gridrows=2)
</source>

{|style="margin: 0 auto;"
| [[Image:CASA5.4.0-Plotms-amp-freq-ea01-02.png|300px|thumb|right|'''Figure 12a''' <br /> Bandpass for antennas ea01 and ea02.]]
| [[Image:CASA5.4.0-Plotms-amp-freq-ea03-04.png|300px|thumb|right|'''Figure 12b''' <br /> Bandpass for antennas ea03 and ea04.]]
| [[Image:CASA5.4.0-Plotms-amp-freq-ea05-07.png|300px|thumb|right|'''Figure 12c''' <br /> Bandpass for antennas ea05 - ea07 (note ea06 is flagged).]]
|}

<br>
</div>
</div>

==== Interactive flagging of bad solutions (calibration tables) ====

[[Image:CASA5.4.0-Plotms-amp-freq-ea01-05-flagging.png|300px|thumb|right|'''Figure 13''' <br /> Interactive plotms flagging of the offset points for ea01 and ea05 in the calibration table.]]
We notice that antennas ea01 and ea05 have a point that is offset from the rest (Figures 2a,c). Let's plot just these two antennas, locate the point on the plot, and flag it interactively through [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms]. The interactive flagging within plotms will not create a backup, therefore it may be wise to use [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagmanager.html flagmanager] before doing so (see Section [[#Backup_Data_-_Flagmanager |Flagmanager]] earlier in this tutorial). 


<source lang="python">
# In CASA
flagmanager(vis='SNR_G55_10s-hanning.initBP', mode='save', versionname='before_flagging')
</source>

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.initBP',xaxis='freq', yaxis='amp', iteraxis='antenna', 
       antenna='ea01,ea05', coloraxis='corr', gridrows=2)
</source>

We will highlight the points by clicking on the <b>Mark Region</b> button, drawing boxes over the points, and clicking on the <b>Flag</b> button. Before doing this, one could also get information on the points by clicking on the Locate button, which will display details about the highlighted regions (Figure 13). After having flagged the offset points, your plots should update.

<div style="background-color: #eeeeee; margin: 40px">
<div style="background-color: #eeeeee; margin: 43px">
<br>

==== Applying calibration ====

We will now apply the bandpass calibration table using [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.calibration.applycal.html applycal].

<source lang="python">
# In CASA
applycal(vis='SNR_G55_10s-hanning.ms', gaintable='SNR_G55_10s-hanning.initBP', calwt=False)
</source>

This operation will flag data that correspond to flagged solutions, so [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.calibration.applycal.html applycal] makes a backup version of the flags prior to operating on the data. Running this task might take a little while.

<br>
</div>
</div>

==== Running RFlag on bandpass calibrated data ====
[[Image:amp_v_freq.beforeRFlag.png|320px|thumb|right|'''Figure 14''' <br />Amplitude vs. Frequency plot of scan 190, before RFlag is applied.]]

Now that we have bandpass-corrected data, we will run [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] in rflag mode.

We will use flagdata with parameters ''mode='rflag','' and ''action='calculate' ''to first review the amount of data to be flagged. We will also change the parameter ''datacolumn='corrected' ''since we've applied the bandpass corrections to the MS and, in the process, created the ''corrected_data'' column in the MS table. 

''' spw 0 '''

First, let's create a plot of our corrected data before we apply RFlag (Figure 14).

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='190' , antenna='ea24', xaxis='freq', yaxis='amp',
       ydatacolumn='corrected', coloraxis='spw', title='Before RFlag', 
       plotfile='amp_v_freq.beforeRFlag.png') 
</source>

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='rflag', spw='0', datacolumn='corrected', 
         action='calculate', display='both', flagbackup=False)
</source>

{|style="margin: 0 auto;"
| [[Image:rflag_default_values.png|400px|thumb|right|'''Figure 15''' <br />RFlag with Default Parameters for scan 22 (use the next scan, next baseline, and next field buttons to see this specific screen).]]
| [[Image:rflag_freq2.5_time3.5.png|400px|thumb|right|'''Figure 16''' <br />RFlag with freqdevscale=2.5, and timedevscale=3.5 for scan 22. We can see more data are being flagged with these more stringent values.]]
|}

After reviewing the calculated flags, we can see that a lot of RFI is being missed (Figure 15). We will need to modify the default parameters for this spectral window. Click on Quit on the lower right hand side of the window. Let's review the parameters for [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] and modify them:

<source lang="python">
# In CASA, get the last called parameter values for flagdata
tget flagdata
</source>

<source lang="python">
# In CASA, inspect the inputs
inp
</source>

The default ''timedevscale=5.0'' and ''freqdevscale=5.0'' parameters are not flagging enough bad data. We can provide more stringent values to the time/freq deviation scales parameters. A value smaller than the default (5.0) will flag more data in either the time or frequency axes, as can be seen on the plots in the displayed window. A value larger than the default will result in less flagged data. 

Since we know spw 0 has lots of RFI, we will change parameters ''freqdevscale=2.5'' and ''timedevscale=3.5''. We will also change parameter ''action='apply'.'' Note that we can always decide that this still isn't good enough and click on <b>Quit</b> to change our parameter values (will not perform flagging). Once the window opens, proceed to scan 22 (Figure 16), review what will be flagged, and click on <b>Stop Display</b> (as we did during TFCrop) to allow the task to continue with the flagging.

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='rflag', spw='0', datacolumn='corrected', 
         freqdevscale=2.5, timedevscale=3.5, action='apply', display='both', flagbackup=False)
</source>
  
Although RFlag has done a pretty good job of finding the bad data, some still remains. One way to excise the remaining bad data is to use the parameter ''mode='extend' ''feature of flagdata, which can extend flags along a chosen axis and removes islands of small data patches in the midst of flagged data. We first extend the flags across polarization so if any one polarization is flagged, all data for that time / channel will be flagged:

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='extend', spw='0', extendpols=True,  
         action='apply', display='', flagbackup=False)
</source>

Now we extend the flags in time and frequency using the parameters ''growtime'' and ''growfreq''.  For this data, the rflag algorithm seems most likely to miss RFI that should be flagged along more of the time axis. We will try with parameter ''growtime=50.0'', which will flag all data for a given channel if more than 50% of that channel's time is already flagged, and parameter ''growfreq=90.0'', which will flag the entire spectrum for an integration if more than 90% of the channels in that integration are already flagged.  

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', mode='extend', spw='0', growtime=50.0, growfreq=90.0, 
         action='apply', display='', flagbackup=False)
</source>

''' spw 1, 2, and 3 '''

Now, let's work on SPW's 1,2, and 3. We've chosen parameter ''display='both' ''in order to first review the flags to decide if too much or too little is being flagged. We can always click on Quit and decide to change parameter values for ''freqdevscale'' and ''timedevscale'' as we did with spectral window 0. Note that spw 2 has more stringent parameter values compared to spw 1 and 3, as it contains more RFI. To allow the flagging to continue, click on <b>Stop Display</b>.

<source lang="python">
# In CASA, run RFlag on spectral windows 1 & 3
flagdata(vis='SNR_G55_10s-hanning.ms', mode='rflag',  spw='1,3', datacolumn='corrected', 
         freqdevscale=4.0, timedevscale=4.0, action='apply', display='both', flagbackup=False)
</source>

<source lang="python">
# In CASA, extend flags in polarization for spectral windows 1 & 3
flagdata(vis='SNR_G55_10s-hanning.ms', mode='extend', spw='1,3', extendpols=True, action='apply', 
         display='', flagbackup=False)
</source>

<source lang="python">
# In CASA, extend flags in time and frequency for spectral windows 1 & 3
flagdata(vis='SNR_G55_10s-hanning.ms', mode='extend', spw='1,3', growtime=50.0, growfreq=90.0, 
         action='apply', display='', flagbackup=False)
</source>

<source lang="python">
# In CASA, run RFlag on spectral window 2 with more RFI, hence smaller frequency and time deviation scale values
flagdata(vis='SNR_G55_10s-hanning.ms', mode='rflag',  spw='2', datacolumn='corrected', 
         freqdevscale=2.5, timedevscale=2.5, action='apply', display='both', flagbackup=False)
</source>

<source lang="python">
# In CASA, extend flags in polarization for spectral window 2
flagdata(vis='SNR_G55_10s-hanning.ms', mode='extend', spw='2', extendpols=True, action='apply',
          display='', flagbackup=False)
</source>

<source lang="python">
# In CASA, extend flags in time and frequency for spectral window 2
flagdata(vis='SNR_G55_10s-hanning.ms', mode='extend', spw='2', growtime=50.0, growfreq=90.0, 
         action='apply', display='', flagbackup=False)
</source>

Let's create an after RFlag plot to see the improvements (Figure 17). Compare the resulting plot to the before TFCrop plot (Figure 14).

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='190' , antenna='ea24', xaxis='freq', yaxis='amp',  
       ydatacolumn='corrected', coloraxis='spw', title='After RFlag', plotfile='amp_v_freq.afterRFlag.png',
       plotrange=[1.2,2,0,2.5])
</source>

{|style="margin: 0 auto;"
| [[Image:amp_v_freq.beforeRFlag.png|350px|thumb|right|'''Figure 14''' <br />Amplitude vs. Frequency plot of scan 190, before RFlag is applied.]]
| [[Image:amp_v_freq.before_after_RFlag.png|350px|thumb|right|'''Figure 17''' <br /> Plot of amplitude vs. frequency of scan 190, after having run RFlag.]]
|}

<b>Summary of flagdata modes tfcrop and rflag</b><br>
Tfcrop algorithim iterates through the data in sections of time, creates a 2D time-frequency (x-y) plane with amplitude in the z axis, one for each baseline and correlation-expression to flag outliers. 
RFlag algorithm also iterates through the data in sections of time, but compares local rms versus global statistics of the data to remove outliers. For more info on TFCrop and RFlag, please see the [https://science.nrao.edu/science/meetings/2016/vla-data-reduction/EVLAWorkshop_RFI_2016_UR.pdf RFI presentation] given at the 5th VLA Data Reduction Workshop.

{| class='wikitable'
|-
!Case
!Tfcrop
!RFlag
|-
| Strong peaks in RFI ||works well.||works well, though continuous RFI (time or frequency) needs tuning.
|-
|Noisy RFI ||Not good for noisy, low level RFI.||works well.
|-
|Broadband RFI ||Not robust, but possible by tuning the polynomial fit (maxnpieces).|| Good if RFI looks noisy. Continuous RFI needs work.
|-
|Non-calibrated data ||Yes, because it can fit for the bandpass.||No, it needs a flat base. Calibration is essential.
|-
|Extended emission|| Yes, since each baseline is treated separately.||high flux on short baselines biases the statistics (use uvrange, or operate on residual data).
|}

== Interactive Flagging ==

To flag data interactively (manually), one can use [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms]. We will be scanning for data points that look odd. Please note that flagging data through plotms will not create a backup, so it's important to use the flagmanager() before deciding to mark your regions for flagging purposes. 

<source lang="python">
# In CASA
flagmanager(vis='SNR_G55_10s-hanning.ms', mode='save',
            versionname='before_interactive_flagging')
</source>

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='50~100', xaxis='uvdist', yaxis='amp',
       ydatacolumn='corrected', coloraxis = 'spw')
</source>

Figure 18 (next section) shows some points in green that have higher amplitudes than the rest. Use the <b>Mark Regions</b> button (square with green plus sign) to highlight the region, and the <b>Locate</b> button (magnifying glass with white page) to obtain information on the data points. We can now decide to flag all of the highlighted area by clicking on the <b>Flag</b> button (red flag). The region is now flagged.


Similarly, one can also perform interactive flagging with [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaviewer.msview.html msview]. Again, the flagging is performed directly on the data, and so it is beneficial to execute flagmanager as above before embarking on interactive flagging with msview(). 

Open msview() and load the data as described in section [[#Identifying_RFI_with_MSview | Identifying RFI with MSview]]:
 
<source lang="python">
# In CASA
msview()
</source>

Select what you would like the axes to display (by default msview will plot time vs baseline), and using zoom tool (magnifying glass button with plus sign) zoom in on the data chunks you would like to inspect and potentially flag. Now, draw a region around the bad data using the <b>drawing selectors</b> (rectangle, circle, polygon) and <b>right-double click</b> to flag. To save the flagging, click <b>Save Edits</b> button in the flagging tab of Data Display Option window. 

<pre>
Flagging data interactively can be useful, but is discouraged, especially for large data volumes.
</pre>

A more proper form of flagging would be to narrow your search on bad data points (Locate data as described above) and use a flagging task to remove them as showed in the next section below.

== Identifying remaining bad data with plotms ==

Once the bulk of the RFI and corrupted data has been removed with the methods described earlier in this guide, it is worth having another look at the data with the visualization tools, either [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaplotms.plotms.html plotms]. This step may be valuable to perform once your data are calibrated and ready for imaging, to double check all the bad data has been indeed removed.

Let's again inspect amplitude vs uv-distance of our calibrated target data (Figure 18) with plotms(). Instead of flagging the data interactively (the Flag button), it is recommended to run the [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casatasks.flagging.flagdata.html flagdata] task. While locating the bad data points in the previous section (<b>Mark Region</b> and then click <b>Locate</b> button), CASA logger provided us with information on the data points. Notice that they all belong to scans 88 and 87. The scans also involve a baseline shared with ea16. To flag these data run the flagdata() task:

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', scan='87,88', antenna='ea16', flagbackup=True)
</source>

To see the effect of this flagging, either Reload the image (tick Reload and click Plot) if your plotms() session from the previous section is still open, or otherwise run the following command:

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='50~100', xaxis='uvdist', yaxis='amp',
       ydatacolumn='corrected', coloraxis = 'spw')
</source>

We can now see the image (Figure 19) looks better without scans 87 and 88 for ea16. 

{|style="margin: 0 auto;"
| [[Image:Corr.Amp_vs_UVdist.png|400px|thumb|right|'''Figure 18''' <br />Amplitude vs. UV-Distance plot for scans 50-100. Outliers have been highlighted to show interactive flagging through plotms.]]
| [[Image:Corr.Amp_vs_UVdist.flagged.png|400px|thumb|right|'''Figure 19''' <br /> Amplitude vs. UV-Distance plot for scans 50-100. Scans 87 and 88 have been flagged for ea16 via flagdata.]]
|}

If you would like to perform these steps with [https://casadocs.readthedocs.io/en/v6.4.1/api/tt/casaviewer.msview.html msview], instead of plotms(), plot <b>time vs. baseline length</b>. Here baseline length is equivalent to the uv-distance.

<!-- Now would be also a good time to play with the plotms parameters and look for more data to flag interactively. As a reminder, at the start of this guide we highlighted and located some of the worst sections with RFI. When reducing/flagging your data, it will prove helpful to review this information and revisit the most RFI affected spectral windows and channels.-->

<!--
=== Amplitude vs. Baseline ===

We will now plot corrected amplitude vs. baseline. We will be looking to flag baselines with consistent high corrected amplitudes as we iterate through each scan. Iterate by clicking on the green arrow buttons on the toolbar within the plotms(). 

<source lang="python">
# In CASA
plotms(vis='SNR_G55_10s-hanning.ms', scan='30,75,120,165,190,235,303', xaxis='baseline', yaxis='amp',
       ydatacolumn='corrected', iteraxis='scan', coloraxis = 'baseline')
</source>
[[Image:corr.amp_vs_baseline_scan75.png|300px|thumb|right|'''Figure 14''' <br /> Amplitude vs. Baseline plot, which is used to try and identify baselines with high amplitudes for mutliple scans.]]

It appears that there are several baselines which have a consistently higher-amplitude than the others, indicating that they're probably contaminated by RFI (Figure 14).  

Use the plotms tools to identify the baselines (see the section [[#Preliminary_Data_Evaluation |Preliminary Data Evaluation]] at the beginning of the guide). Iterate through to the different scans to verify that these higher amplitudes correspond to the same baselines. We will flag several of them: ea04&ea16, ea02&ea08, and ea02&ea27. 

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', antenna='ea04&ea16', spw='1', flagbackup=False)
</source>

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', antenna='ea02&ea27', spw='1', flagbackup=False)
</source>

<source lang="python">
# In CASA
flagdata(vis='SNR_G55_10s-hanning.ms', antenna='ea02&ea08', spw='1', flagbackup=False)
</source>
-->

== Flagging Summary & Report ==

We will now run flagdata in summary mode to inspect how much total data has been flagged. We can also create a plot of the percentage of flagged data with respect to frequency by setting parameter ''display='report' ''(Figure 20). The report parameter will also create a plot of the antennas, with the circle size representing the percentage of flagged data per antenna (Figure 21). This can be viewed by clicking Next. One can also zoom in and out for a better view.

Note: Currently there is a graphical bug with how the 'Total percentage of flagged data vs. frequency plot' is drawn in CASA 6.4.1. We have left the previous versions of the plots here as an example. A fix for this is in the works and should be avaliable in the future.

<source lang="python">
# In CASA
flagInfo = flagdata(vis='SNR_G55_10s-hanning.ms', mode='summary', action='calculate', display='report', spwchan=True)
</source><br />

<source lang="python">
# In CASA
print("\n %2.1f%% of G55.7+3.4, %2.1f%% of 3C147, and %2.1f%% of J1925+2106 are flagged. \n" %
     (100.0 * flagInfo['field']['G55.7+3.4']['flagged'] / flagInfo['field']['G55.7+3.4']['total'],
     100.0 * flagInfo['field']['0542+498=3C147']['flagged'] / flagInfo['field']['0542+498=3C147']['total'],
     100.0 * flagInfo['field']['J1925+2106']['flagged'] / flagInfo['field']['J1925+2106']['total']))
</source><br />

<source lang="python">
# In CASA
%cpaste

# Press Enter or Return, then copy/paste the following:
print("Spectral windows are flagged as follows:")

for spw in range(0,4):
     print("SPW %s: %2.1f%%" % (spw, 100.0 * flagInfo['spw'][str(spw)]['flagged'] / flagInfo['spw'][str(spw)]['total']))
--
</source>

{|style="margin: 0 auto;"
| [[Image:Percent.Flagged.Plot.png|400px|thumb|right|'''Figure 20''' <br /> Total percentage of flagged data vs. frequency, colorized by spectral window.]]
| [[Image:Percent.Flagged.Ant.png|400px|thumb|right|'''Figure 21''' <br /> Total Percentage of data flagged from each antenna. A larger circle represents more flagged data for that antenna. ]]
|}

As a result of the flagging we have removed over 40% of the data for G55.7+3.4 and, as expected, spectral windows 0 and 2 have the most flagged data.

In addition, we can inspect the CASA log, which will report the percentage of flagged data for: <br />
1. per Spw/ per Channel <br />
2. Each Antenna <br />
3. Every Correlation (RR, RL, LL, LR) <br />
4. Every Scan <br />
5. Every spectral window <br />

[[Main Page | &#8629; '''CASAguides''']]

== Extracted Scripts for VLA CASA Flagging 6.5.4 ==
[[Media:VLA_CASA_FLAGGING-CASA6.5.4.txt|VLA_CASA_FLAGGING-CASA6.5.4.txt]]


{{Checked 6.5.4}}

</div>

<!--
--Original: Miriam Hartman <br />
--Modifications: Lorant Sjouwerman (4.4.0, 2015/07/07) <br />
--Modifications: Juergen Ott (4.5.2, 2016/04/13) <br />
--Topical Guide: Jose Salcido (4.5.2, 2016/04/15) <br />
--Edits: Tony Perreault (4.5.2, 2016/05/25) <br />
--Edits: Tony Perreault (4.7.0, 2016/10/14) <br />
--Edits: Jose Salcido (4.7.0, 2016/10/26) <br />
--Edits: Tony Perreault (4.7.0, 2016/10/26 <br />
--Edits: Anna Kapinska (5.4.0, 2018/11/30 <br />
--Edits: Angelica Vargas (5.5.0, 2019/06/24 <br />
--Edits: Aaron Lawson (5.7.0, 2020/09/28 <br />
--Edits: Efrain Rodriguez Arzaga (6.5.4, 2024/03/01 <br />