pyxisMs2mat package

Set of helper functions to extract useful data from a MS Table into a set a .mat file compatible with the interface of this library. Examples are provided below.

List of modules

Module pyxisMs2mat.pyxis4DataExtraction

Requirements

The pyxisMs2mat.pyxis4DataExtraction module requires the two following Python packages.

Casacore: https://github.com/casacore/casacore
Meqtrees: https://github.com/ratt-ru/meqtrees/wiki/Installation

General notes

Data extraction is performed using pyxis. The task should be performed in the directory $FHS/pyxisMs2mat, which contains the python script pyxis4DataExtraction.py.
Extracted .mat files are saved in $FHS/data/. The files contain the following fields.

"frequency"  % channel frequency
"y"  % data (Stokes I)
"u"  % u coordinate (in units of the wavelength)
"v"  % v coordinate (in units of the wavelength)
"w"  % w coordinate (in units of the wavelength)
"nW"  % sqrt(weights)
"nWimag" % imaging weights if available (Briggs or uniform), empty otherwise
"maxProjBaseline"  % max projected baseline (in units of the wavelength)

Output channels’ indices and their associated filenames are incremented by 1 for MATLAB indexing purposes.
Functions provided in pyxisMs2mat.pyxis4DataExtraction are given as examples. The user is encouraged to define new functions tailored to the structure of his measurement set in case it is organised differently.
In case of multiple spectral windows, the user is advised to use the split task in CASA to image specific spectral windows and extract the data from the resulting measurement subset.

Examples

Single measurement set (MS)

Extracting data from the channels indexed from 0 to 3 of the source with field ID 0, from all spectral windows.

The user must provide the name/path to the measurement set $MS. The following inputs are optional.

$SRCNAME  # default SRCNAME="" : source nametag which defines the main directory of the extracted data.
$MSTAG    # default MSTAG="" : nametag of the data set which defines the subdirectory of the extracted data. It needs to be set when multiple data sets of the source of interest are available.
$FIELDID  # default FIELDID=0 : field ID of the source of interest,
$FIRSTCH  # default FIRSTCH=0 : ID of the first channnel to be extracted from each spectral window,
$LASTCH   # default  LASTCH=NUM_CHAN : ID of the last channnel to be extracted from each spectral window

Note

In $FHS/imaging/main_input_imaging.m, the user should set the name of the image cube to be reconstructed srcName to the same value as $SRCNAME

From the terminal, execute:

cd   $FHS/pyxisMs2mat
pyxis MS=myms.ms  SRCNAME=cyga FIRSTCH=0  LASTCH=3 FIELDID=0 getdata_ms

Data will be saved as .mat files in the directory $FHS/data/cyga/. In the case of a single spectral window, the outcome is as follows

data/cyga/data_ch_1.mat
data/cyga/data_ch_2.mat
data/cyga/data_ch_3.mat
data/cyga/data_ch_4.mat

Note

In $FHS/imaging/main_input_imaging.m, if the data set nametag ($MSTAG) was not provided during data extraction, as in the example above, the user should set datasetNames as

datasetNames = {''};

Combine two measurement sets at two consecutive frequency bandwidths, with same spectral window specs

Extracting data from the channels indexed from 0 to 15 of the source with field ID 2, from all spectral windows.

The user must provide the name/path to the two measurement sets $MSLOW and $MSHIGH associated with the low frequency band and high frequency band meaurement sets, respectively. The following inputs are optional.

$SRCNAME  # default SRCNAME="" : source nametag which defines the main directory of the extracted data.
$MSTAG    # default MSTAG="" : nametag of the data set which defines the subdirectory of the extracted data. It needs to be set when multiple data sets of the source of interest are available.
$FIELDID  # default FIELDID=0 : field ID of the source of interest,
$FIRSTCH  # default FIRSTCH=0 : ID of the first channnel to be extracted from each spectral window,
$LASTCH   # default  LASTCH=NUM_CHAN : ID of the last channnel to be extracted from each spectral window

From the terminal, execute:

cd   $FHS/pyxisMs2mat
pyxis MSLOW=mylowbandms.ms MSHIGH=myhighbandms.ms SRCNAME=cyga FIRSTCH=0 LASTCH=15 FIELDID=2  getdata_ms_concat_bandwidth

Data will be saved as .mat files in the directory $FHS/data/cyga/.

In the case of a single spectral window, the outcome is as follows

data/cyga/data_ch_1.mat  % channel 1 from mylowbandms.ms
.
data/cyga/data_ch_16.mat % channel 16 from mylowbandms.ms
data/cyga/data_ch_17.mat % channel 1 from myhighbandms.ms
.
data/cyga/data_ch_32.mat % channel 16 from myhighbandms.ms

Combine different measurment sets spanning the same frequency bandwidth, with same spectral window specs

Extracting data from the channels indexed from 0 to 12 of the source with field ID 0, from all spectral windows. From the terminal, execute:

cd   $FHS/pyxisMs2mat
pyxis MS=myms1.ms  SRCNAME=cyga MSTAG=dataset1 FIRSTCH=0  LASTCH=12 FIELDID=0 getdata_ms \
pyxis MS=myms2.ms  SRCNAME=cyga MSTAG=dataset2 FIRSTCH=0  LASTCH=12 FIELDID=0 getdata_ms \
pyxis MS=mymsn.ms  SRCNAME=cyga MSTAG=datasetn FIRSTCH=0  LASTCH=12 FIELDID=0 getdata_ms \

Data sets will be saved in the sub-directories.

data/cyga/dataset1/
data/cyga/dataset2/
data/cyga/datasetn/

Note

In $FHS/imaging/main_input_imaging.m, the user should provide the nametags of the different sets in a cell as input to combine the data sets during imaging.

datasetNames = {'dataset1', 'dataset2','datasetn'};