Command-line tools

General

Flag RFI with AOFlagger

Run AOFlagger on a Measurement Set (MS).

usage: low_flag_rfi [-h] [--rfi-strategy {comprehensive,fast,extended}]
                    [--chunk-size CHUNK_SIZE]
                    ms_path

Positional Arguments

ms_path: Path to the Measurement Set

Named Arguments

--rfi-strategy

Possible choices: comprehensive, fast, extended

Optional packaged AOFlagger strategy to use.

--chunk-size

AOFlagger chunk size in timesteps. Default: 1800.

Default: 1800

(De)Rotate visibilities

usage: low_vis_rotate [-h] [-c COLUMN] [-w WRITE_TO_COLUMN]
                      [-m {ground,analytic,oskardipole,eep}] [-i] [-d]
                      [--eepdir EEPDIR] [--eepbase EEPBASE]
                      [--eepsuff EEPSUFF] [--eepcorr]
                      msname [msname ...]

Positional Arguments

msname: Name of MS. This can be a wildcard string. If more than one MS name matches, the process will run for each of them one at a time.

Named Arguments

-c, --column

MS column name to read. This is also the column that will be written to if not –dryrun, and unless –write_to_column is used.

Default: 'CORRECTED_DATA'

-w, --write_to_column

Write result to another column? (USE WITH CAUTION) [default value of COLUMN argument]

-m, --mode

Possible choices: ground, analytic, oskardipole, eep

Conversion mode. Choose from “ground” rotation (not recommended), “analytic”, “oskardipole”, or “eep”.

Default: 'analytic'

-i, --invert

Invert sense of rotation? Use this option if you are forward modeling (applying to MODEL_DATA) or undoing a previously-applied rotation.

Default: False

-d, --dryrun

Only compute the rotations but do not write back into the MS? Useful with -p.

Default: False

--eepdir

EEP base directory. Ignored unless MODE is EEP.

Default: /shared/eep-data/Perturbed_Vogel_HARP/Average_EEPs

--eepbase

EEP filename base. Ignored unless MODE is EEP.

Default: 'HARP_SKALA41_randvogel_avg_'

--eepsuff

EEP filename suffix. Ignored unless MODE is EEP.

Default: '.npz'

--eepcorr

Apply the EEP PA correction? Ignored unless MODE is EEP.

Default: False

Generate a GLEAM Sky Model

Create AO calibration model from MS.

usage: low_gleam_model [-h] [-o OUTPUT_PATH] [-m {csv,skymodel}]
                       [-s {single,wide}] [-f REFFREQ] [-r RADIUS]
                       ms_path

Positional Arguments

ms_path: Path to the measurement set.

Named Arguments

-o, --output-path

Path to save the AO calibration model.

-m, --model-type

Possible choices: csv, skymodel

Type of model to create.

Default: 'csv'

-s, --sky-type

Possible choices: single, wide

Type of sky model to create. ‘single’ will create a single source mode. Wide will sample many, attenudated by the beam.

Default: 'single'

-f, --reffreq

Reference frequency in MHz

-r, --radius

Search radius for sources in degrees

Default: 1

Get a field name

Get field name from a Measurement Set (MS).

usage: low_get_field_name [-h] [--field-index FIELD_INDEX] ms_path

Positional Arguments

ms_path: Path to the Measurement Set (MS) directory.

Named Arguments

--field-index

Index of the field to retrieve the name for.

Default: 0

Convert a CASA delay calibration table to text

Convert a CASA caltable to a text file

usage: low_delay_table_to_txt [-h] caltable

Positional Arguments

caltable: Path to calibration table(s).

Run calibration with SDP tools

Plotting

Plot AOCalibrate solutions

Run calibrate and apply the solutions given a measurement set and sky-model.

usage: low_aocalibrate_plot [-h] [--ref-ant REF_ANT] [--ms MS] aosolutions

Positional Arguments

aosolutions: Path to the solution file to inspect and plot

Named Arguments

--ref-ant

The reference antenna to use when plotting the bandpass solutions. If -1, the best one will be selected.

Default: -1

--ms

The measurement set to use when plotting the bandpass solutions.

Plot baseline spectra

Plot visibilities per baseline.

usage: low_plot_baselines [-h] [--out-dir OUT_DIR] [--no-fast-plot]
                          [--norm {lin,log,sqrt}]
                          [--plot-type {spectrum,delay,delay-rate}]
                          [--data-column DATA_COLUMN]
                          [--data-type {amp,phase,real,imag}]
                          [--max-concurrent MAX_CONCURRENT]
                          [--max-baselines MAX_BASELINES]
                          ms_path

Positional Arguments

ms_path: Path to visibilities.

Named Arguments

--out-dir

Output directory for plots. Defaults to the MS directory.

--no-fast-plot

Use pcolormesh instead of pcolorfast.

Default: False

--norm

Possible choices: lin, log, sqrt

Plot normalisation.

Default: 'lin'

--plot-type

Possible choices: spectrum, delay, delay-rate

Type of plot.

Default: 'spectrum'

--data-column

Data column to plot.

Default: 'DATA'

--data-type

Possible choices: amp, phase, real, imag

Type of data to plot.

Default: 'amp'

--max-concurrent

Number of worker processes.

Default: 4

--max-baselines

Maximum number of baselines to plot.

Plot fringes

Plot fringes per for all baselines.

usage: low_plot_fringes [-h] [--out-dir OUT_DIR]
                        [--pols {XX,XY,YX,YY} [{XX,XY,YX,YY} ...]]
                        [--freq-min-mhz FREQ_MIN_MHZ]
                        [--freq-max-mhz FREQ_MAX_MHZ] [--spw-id SPW_ID]
                        [--max-baselines MAX_BASELINES]
                        [--show-coarse-channels]
                        [--coarse-channel-min COARSE_CHANNEL_MIN]
                        [--coarse-channel-max COARSE_CHANNEL_MAX]
                        [--data-column DATA_COLUMN]
                        ms_path

Positional Arguments

ms_path: Path to visibilities.

Named Arguments

--out-dir

Output directory for plots. Defaults to the MS directory.

--pols

Possible choices: XX, XY, YX, YY

Polarisations to plot.

--freq-min-mhz

Minimum frequency in MHz.

Default: 0

--freq-max-mhz

Maximum frequency in MHz.

Default: inf

--spw-id

Spectral window ID.

Default: 0

--max-baselines

Maximum number of baselines to plot.

--show-coarse-channels

Overlay coarse channel boundaries on the plot.

Default: False

--coarse-channel-min

Minimum coarse channel index.

Default: 0

--coarse-channel-max

Maximum coarse channel index.

Default: 512

--data-column

Data column

Default: 'DATA'

Plot animated fringes for single baseline

Make an animation (default = GIF) of amplitudes an phases for a given baseline over time

usage: low_animate_fringes [-h] [--tfactor TFACTOR] [--ffactor FFACTOR]
                           [--rad] [--linear] [--delay_samples DELAY_SAMPLES]
                           [--intra_chan_delay_samples INTRA_CHAN_DELAY_SAMPLES]
                           [--output_animation OUTPUT_ANIMATION] [--pols POLS]
                           ms_path stations stations

Positional Arguments

ms_path: Path to visibilities
stations: The two stations comprising the desired baseline

Named Arguments

--tfactor

Number of time bins to average together (default: do no averaging)

Default: 1

--ffactor

Number of channels to average together (default: do no averaging)

Default: 1

--rad

Plot phase angles in radians instead of the default degrees

Default: False

--linear

Plot amplitudes on a linear scale instead of the default log scale

Default: False

--delay_samples

Apply an overall phase slope across all channels corresponding to a delay of DELAY_SAMPLES*1.08us of pre-channelised data

Default: 0

--intra_chan_delay_samples

Apply a phase slope across coarse channels corresponding to a delay of DELAY_SAMPLES*1.08us of post-channelised data

Default: 0

--output_animation

Output (path to) file name where the animation gets written (default = ‘STATION1_STATION2_anim.gif’). If given the special value SHOW, then plt.show() is called instead of writing the result to file.

--pols

Comma-separated list of polarisations to plot. Supported polarisations are (‘XX’, ‘XY’, ‘YX’, ‘YY’).

Default: 'XX,YY'

Plot fringe rates across baselines

Plot phase vs time over baselines per station.

usage: low_plot_fringerate [-h] [--out-dir OUT_DIR] [--freq-mhz FREQ_MHZ]
                           [--bw-mhz BW_MHZ] [--uv-min-m UV_MIN_M]
                           [--data-column DATA_COLUMN]
                           ms_path

Positional Arguments

ms_path: Path to visibilities.

Named Arguments

--out-dir

Output directory for plots. Defaults to the MS directory.

--freq-mhz

Frequency to select in MHz or special valuues of ‘start’, ‘mid’, or ‘end’

Default: mid

--bw-mhz

Bandwidth to average over in MHz

Default: 1

--uv-min-m

Minimum UV distance in metres for a baseline to be included

Default: 500

--data-column

Data column to plot.

Default: 'DATA'

MS Fixes

Reverse baseline antenna ordering

Reverse baseline ordering in a MeasurementSet

usage: low_reverse_baselines [-h] [-c CHUNKSIZE] [-d] ms_path

Positional Arguments

ms_path: Path to MS file

Named Arguments

-c, --chunksize

Number of rows to process in a chunk

Default: 1000

-d, --dry-run

Do not execute baseline reversal - just check the ANTENNA1/2 ordering

Default: False

Add a subtable to an MS

Copy an existing table (e.g. PHASED_ARRAY) to another table as a subtable

usage: low_add_subtable [-h] [-d] [-f] [-n NAME] ms subtable

Positional Arguments

ms: Path to target MeasurementSet
subtable: Path to subtable to add

Named Arguments

-d, --dry-run

Dry run

Default: False

-f, --force

Force the subtable to be replaced

Default: False

-n, --name

Set telescope name

Rename the telescope in an MS

Rename TELESCOPE_NAME in a MeasurementSet

usage: low_rename_telescope [-h] [-n NAME] ms_path

Positional Arguments

ms_path: Path to target MeasurementSet

Named Arguments

-n, --name

Set telescope name

Default: 'SKA-LOW'

Fix WEIGHT/WEIGHT_SPECTRUM tables

Fix WEIGHT/WEIGHT_SPECTRUM column using FD, INTERVAL, and channel bandwidth in MS

usage: low_fix_weights [-h] [-c CHUNKSIZE] [-d] ms_path

Positional Arguments

ms_path: Path to target MeasurementSet

Named Arguments

-c, --chunksize

Number of rows to process in a chunk

Default: 1000

-d, --dry-run

Do not write new columns to MS

Default: False

Fix INTERVAL table

Fix INTERVAL column using TIME in MS

usage: low_fix_interval [-h] ms_path

Positional Arguments

ms_path: Path to target MeasurementSet