Advanced CLI

Calibration related CLI

1. Flagging of calibrators, use run-mwa-flag .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-flag [-h] [--workdir WORKDIR] [--outdir OUTDIR]
                    [--datacolumn DATACOLUMN] [--no_flag_bad_ants]
                    [--no_flag_bad_spw] [--use_tfcrop] [--use_rflag]
                    [--no_flag_autocorr] [--no_flag_quack] [--no_flagbackup]
                    [--run_solarflagger] [--normalize] [--threshold THRESHOLD]
                    [--flagdimension FLAGDIMENSION] [--no_restore] [--verbose]
                    [--jobid JOBID] [--cpu_frac CPU_FRAC]
                    [--mem_frac MEM_FRAC]
                    mslist metafits

Initial flagging

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Name of measurement sets (Comma seperated)
  metafits              Metafits file
  --workdir WORKDIR     Name of work directory (default: )
  --outdir OUTDIR       Name of output directory (default: )
  --datacolumn DATACOLUMN
                        Name of the datacolumn (default: DATA)

###################
Advanced parameters
###################:
  --no_flag_bad_ants    Do not flag bad antennas
  --no_flag_bad_spw     Do not flag bad spectral windows
  --use_tfcrop          Use tfcrop flagging
  --use_rflag           Use rflag flagging
  --no_flag_autocorr    Do not flag auto-correlations
  --no_flag_quack       Do not flag quack timestamps
  --no_flagbackup       Do not backup flags
  --run_solarflagger    Run solar flagger or not
  --normalize           Use normalization in solar flagger or not
  --threshold THRESHOLD
                        Flag threshold (default: 5.0)
  --flagdimension FLAGDIMENSION
                        Flag dimension (default: freqtime)
  --no_restore          Do not restore flags
  --verbose             Verbose logs
  --jobid JOBID         Job ID (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   CPU fraction to use (default: 0.8)
  --mem_frac MEM_FRAC   Memory fraction to use (default: 0.8)

1. Simulate visibilities for calibrators, use run-mwa-import-model .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-import-model [-h] --workdir WORKDIR [--beamfile BEAMFILE]
                            [--sourcelist SOURCELIST] [--verbose]
                            [--jobid JOBID] [--cpu_frac CPU_FRAC]
                            [--mem_frac MEM_FRAC]
                            mslist metafits

Simulate and import MWA visibilities

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Name of the measurement sets (comma seperated)
  metafits              Name of the metafits file
  --workdir WORKDIR     Work directory

###################
Advanced parameters
###################:
  --beamfile BEAMFILE   Name of the MWA PB file
  --sourcelist SOURCELIST
                        Source model file
  --verbose             Verbose logs
  --jobid JOBID         Job ID

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   CPU fraction
  --mem_frac MEM_FRAC   Memory fraction

3. Perform basic calibration, use run-mwa-basic-cal .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-basic-cal [-h] --workdir WORKDIR [--outdir OUTDIR]
                         [--refant REFANT] [--uvrange UVRANGE]
                         [--no_perform_polcal] [--keep_backup] [--verbose]
                         [--jobid JOBID] [--cpu_frac CPU_FRAC]
                         [--mem_frac MEM_FRAC]
                         mslist metafits

Basic calibration using calibrator fields

options:
  -h, --help           show this help message and exit

###################
Essential parameters
###################:
  mslist               Name of measurement sets (comma separated)
  metafits             Metafits file
  --workdir WORKDIR    Working directory for calibration outputs (default:
                       auto-created next to MS) (default: )
  --outdir OUTDIR      Output directory (default: auto-created in the workdir)
                       (default: )

###################
Advanced calibration parameters
###################:
  --refant REFANT      Reference antenna (default: )
  --uvrange UVRANGE    UV range for calibration (e.g. '>100lambda') (default:
                       )
  --no_perform_polcal  Disable polarization calibration
  --keep_backup        Keep backup of measurement set after each calibration
                       round
  --verbose            Verbose logs
  --jobid JOBID        Job ID for logging and PID tracking (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC  CPU fraction to use (default: 0.8)
  --mem_frac MEM_FRAC  Memory fraction to use (default: 0.8)

4. Apply basic calibration solutions, use run-mwa-apply-basiccal .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-apply-basiccal [-h] --target_metafits TARGET_METAFITS --workdir
                              WORKDIR --caldir CALDIR [--applymode APPLYMODE]
                              [--only_amplitude] [--overwrite_datacolumn]
                              [--force_apply] [--verbose] [--jobid JOBID]
                              [--cpu_frac CPU_FRAC] [--mem_frac MEM_FRAC]
                              mslist

Apply basic calibration solutions to target scans

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Comma-separated list of measurement sets (required)
  --target_metafits TARGET_METAFITS
                        Target metafits file (default: )
  --workdir WORKDIR     Working directory for intermediate files (default: )
  --caldir CALDIR       Directory containing calibration tables (default: )

###################
Advanced parameters
###################:
  --applymode APPLYMODE
                        Applycal mode (e.g. 'calonly', 'calflag') (default:
                        calflag)
  --only_amplitude      Apply only amplitude
  --overwrite_datacolumn
                        Overwrite corrected data column in MS
  --force_apply         Force apply calibration even if already applied
  --verbose             Verbose logs
  --jobid JOBID         Job ID for logging and process tracking (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   CPU fraction to use (default: 0.8)
  --mem_frac MEM_FRAC   Memory fraction to use (default: 0.8)

5. Split measurement set for self-calibration or final imaging, use run-mwa-split .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-split [-h] [--workdir WORKDIR] [--datacolumn DATACOLUMN]
                     [--scan SCAN] [--time_window TIME_WINDOW]
                     [--time_interval TIME_INTERVAL]
                     [--quack_timestamps QUACK_TIMESTAMPS] [--freqres Float]
                     [--timeres Float] [--prefix PREFIX] [--force_split]
                     [--verbose] [--jobid JOBID] [--cpu_frac Float]
                     [--mem_frac Float]
                     mslist metafits

Split measurement set into coarse channels

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Name of measurement sets (required positional
                        argument)
  metafits              Metafits file (required positional argument)
  --workdir WORKDIR     Name of work directory (default: )

###################
Advanced parameters
###################:
  --datacolumn DATACOLUMN
                        Data column to split (default: data)
  --scan SCAN           Target scan to split (default: 1)
  --time_window TIME_WINDOW
                        Time window in seconds of a single time chunk
                        (default: -1)
  --time_interval TIME_INTERVAL
                        Time interval in seconds between two time chunks
                        (default: -1)
  --quack_timestamps QUACK_TIMESTAMPS
                        Time stamps to ignore at the start and end of the each
                        scan (default: -1)
  --freqres Float       Frequency to average in MHz (default: -1)
  --timeres Float       Time bin to average in seconds (default: -1)
  --prefix PREFIX       Splited ms prefix name (default: targets)
  --force_split         Force to split
  --verbose             Verbose logs
  --jobid JOBID         Job ID (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac Float      CPU fraction to use (default: 0.8)
  --mem_frac Float      Memory fraction to use (default: 0.8)

6. Perform self-calibration, use run-mwa-selfcal .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-selfcal [-h] --workdir WORKDIR --caldir CALDIR
                       [--no_cal_applied] [--start_thresh Float]
                       [--stop_thresh Float] [--max_iter Integer]
                       [--max_DR Float] [--intselfcal_min_iter Integer]
                       [--polselfcal_min_iter Integer] [--conv_frac Float]
                       [--solint SOLINT] [--uvrange UVRANGE] [--minuv Float]
                       [--weight WEIGHT] [--robust Float] [--applymode String]
                       [--min_tol_factor Float] [--no_apcal] [--no_polcal]
                       [--no_solar_selfcal] [--use_solarflagger]
                       [--keep_backup] [--verbose] [--jobid JOBID]
                       [--cpu_frac Float] [--mem_frac Float]
                       mslist metafits

Self-calibration

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Comma-separated list of measurement sets (required
                        positional argument)
  metafits              Metafits file
  --workdir WORKDIR     Working directory (default: )
  --caldir CALDIR       Caltable directory (default: )

###################
Advanced calibration and imaging parameters
###################:
  --no_cal_applied      Basic calibration is not applied
  --start_thresh Float  Starting CLEANing threshold (default: 5)
  --stop_thresh Float   Stop CLEANing threshold (default: 3)
  --max_iter Integer    Maximum number of selfcal iterations (in each mode,
                        phaseonly, amplitude-phase, polselfcal) (default: 30)
  --max_DR Float        Maximum dynamic range (default: 100000)
  --intselfcal_min_iter Integer
                        Minimum number of intensity selfcal iterations
                        (default: 3)
  --polselfcal_min_iter Integer
                        Minimum number of polarisation selfcal iterations
                        (default: 5)
  --conv_frac Float     Fractional change in DR to determine convergence
                        (default: 0.1)
  --solint SOLINT       Solution interval (default: 60s)
  --uvrange UVRANGE     Calibration UV-range (CASA format) (default: )
  --minuv Float         Minimum UV-lambda used for imaging (default: 0)
  --weight WEIGHT       Imaging weight (default: briggs)
  --robust Float        Robust parameter for briggs weight (default: 0.0)
  --applymode String    Solution apply mode (default: calonly)
  --min_tol_factor Float
                        Minimum tolerable variation in temporal direction in
                        percentage (default: 1.0)
  --no_apcal            Do not perform ap-selfcal
  --no_polcal           Do not perform polarisation selfcal
  --no_solar_selfcal    Do not perform solar self-calibration
  --use_solarflagger    Use solar flagger or not
  --keep_backup         Keep backup of self-calibration rounds
  --verbose             Verbose logs
  --jobid JOBID         Job ID (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac Float      CPU fraction to use (default: 0.8)
  --mem_frac Float      Memory fraction to use (default: 0.8)

7. Apply self-calibration solutions, use run-mwa-apply-selfcal .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-apply-selfcal [-h] --workdir WORKDIR --caldir CALDIR
                             [--applymode APPLYMODE] [--overwrite_datacolumn]
                             [--force_apply] [--verbose] [--jobid JOBID]
                             [--cpu_frac CPU_FRAC] [--mem_frac MEM_FRAC]
                             mslist metafits

Apply self-calibration solutions to target scans

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Comma-separated list of measurement sets (required)
  metafits              Metafits file (required)
  --workdir WORKDIR     Working directory for intermediate files (default: )
  --caldir CALDIR       Directory containing self-calibration tables (default:
                        )

###################
Advanced parameters
###################:
  --applymode APPLYMODE
                        Applycal mode (e.g. 'calonly', 'calflag') (default:
                        calonly)
  --overwrite_datacolumn
                        Overwrite corrected data column in MS
  --force_apply         Force apply calibration even if already applied
  --verbose             Verbose logs
  --jobid JOBID         Job ID for logging and PID tracking (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   CPU fraction to use (default: 0.8)
  --mem_frac MEM_FRAC   Memory fraction to use (default: 0.8)

8. Move phasecenter to solar center, use run-mwa-movetosun .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-movetosun [-h] [--workdir WORKDIR] [--verbose] [--jobid JOBID]
                         [--cpu_frac CPU_FRAC] [--mem_frac MEM_FRAC]
                         mslist

Move phasecenter of the measurement set to the Sun

options:
  -h, --help           show this help message and exit

###################
Essential parameters
###################:
  mslist               Measurement set list, comma seperated
  --workdir WORKDIR    Name of work directory (default: )

###################
Advanced parameters
###################:
  --verbose            Verbose logs
  --jobid JOBID        Job ID (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC  CPU fraction to use (default: 0.8)
  --mem_frac MEM_FRAC  Memory fraction to use (default: 0.8)

MWA specific CLI

1. Make frequency interpolated MWA primary beam, use run-mwa-beam-interpolate .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-beam-interpolate [-h] [--freqres FREQRES] mwapb_file

Interpolate MWA primary beam coefficients at finer spectral resolution

options:
  -h, --help         show this help message and exit

###################
Essential parameters
###################:
  mwapb_file         Original MWA primary beam coefficient file
  --freqres FREQRES  Frequency resolution of the interpolated file in kHz
                     (default: 160)

Solar specific CLI

1. To correct sidereal motion of the Sun, if the Sun is not tracked by the correlator delay center, use run-mwa-solar-siderealcor . This is useful for observations where the Sun is in sidelobe of the telescope primary beam.

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-solar-siderealcor [-h] [--workdir WORKDIR] [--verbose]
                                 [--jobid JOBID] [--cpu_frac Float]
                                 [--mem_frac Float]
                                 mslist

Correct measurement sets for sidereal motion

options:
  -h, --help         show this help message and exit

###################
Essential parameters
###################:
  mslist             Comma-separated list of measurement sets (required
                     positional argument)
  --workdir WORKDIR  Working directory (default: )

###################
Advanced calibration and imaging parameters
###################:
  --verbose          Verbose logs
  --jobid JOBID      Job ID (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac Float   CPU fraction to use (default: 0.8)
  --mem_frac Float   Memory fraction to use (default: 0.8)

2. Make dynamic spectra of solar scans, use run-mwa-makeds .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-makeds [-h] --workdir WORKDIR --outdir OUTDIR
                      [--plot_quantity PLOT_QUANTITY] [--extension EXTENSION]
                      [--overwrite] [--verbose] [--jobid JOBID]
                      [--cpu_frac CPU_FRAC] [--mem_frac MEM_FRAC]
                      mslist metafits

Make MWA dynamic spectra of the Sun

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Measurement set list (comma seperated)
  metafits              Metafits file
  --workdir WORKDIR     Working directory (default: None)
  --outdir OUTDIR       Output directory (default: None)

###################
Advanced parameters
###################:
  --plot_quantity PLOT_QUANTITY
                        Plot quantity (TB ot flux) (default: TB)
  --extension EXTENSION
                        Save file extension (default: png)
  --overwrite           Overwrite existing plot or not
  --verbose             Verbose logs
  --jobid JOBID         Job ID for logging and PID tracking (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   Fraction of CPU usuage per node (default: 0.8)
  --mem_frac MEM_FRAC   Fraction of memory usuage per node (default: 0.8)

3. Make overlays on EUV images, use run-mwa-euvoverlay .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-euvoverlay [-h] [--workdir WORKDIR] [--all_overlay] [--verbose]
                          [--jobid JOBID] [--cpu_frac CPU_FRAC]
                          [--mem_frac MEM_FRAC]
                          imagedir outdir

Overlay MWA images on EUV images

options:
  -h, --help           show this help message and exit

###################
Essential parameters
###################:
  imagedir             Image directory
  outdir               Overlay output directory
  --workdir WORKDIR    Work directory (default: )

###################
Advanced parameters
###################:
  --all_overlay        Make overlays of all images
  --verbose            Verbose logs
  --jobid JOBID        Job ID (default: 0)

###################
Resource parameters
###################:
  --cpu_frac CPU_FRAC
  --mem_frac MEM_FRAC

Imaging related CLI

1. Perform spectro-polarimetric snapshot imaging, use run-mwa-imaging .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-imaging [-h] --workdir WORKDIR [--outdir OUTDIR]
                       [--freqrange FREQRANGE] [--timerange TIMERANGE]
                       [--datacolumn DATACOLUMN] [--pol POL]
                       [--freqres FREQRES] [--timeres TIMERES]
                       [--weight WEIGHT] [--robust ROBUST] [--minuv_l MINUV]
                       [--threshold THRESHOLD] [--cutout_rsun CUTOUT_RSUN]
                       [--no_multiscale] [--no_solar_mask] [--no_savemodel]
                       [--no_saveres] [--no_make_plots] [--cpu_frac CPU_FRAC]
                       [--mem_frac MEM_FRAC] [--jobid JOBID]
                       mslist

Perform spectropolarimetric snapshot imaging

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  mslist                Comma-separated list of measurement sets (required)
  --workdir WORKDIR     Work directory for imaging (default: )
  --outdir OUTDIR       Output directory for imaging products (default: )

###################
Advanced imaging parameters
###################:
  --freqrange FREQRANGE
                        Frequency range to image (default: )
  --timerange TIMERANGE
                        Time range to image (default: )
  --datacolumn DATACOLUMN
                        Data column to use for imaging (default:
                        CORRECTED_DATA)
  --pol POL             Stokes parameters to image (default: I)
  --freqres FREQRES     Frequency resolution per chunk in MHz (-1 for full)
                        (default: -1)
  --timeres TIMERES     Time resolution per chunk in seconds (-1 for full)
                        (default: -1)
  --weight WEIGHT       Imaging weighting scheme (default: briggs)
  --robust ROBUST       Briggs robust parameter (default: 0.0)
  --minuv_l MINUV       Minimum UV distance in wavelengths (default: 0)
  --threshold THRESHOLD
                        CLEAN threshold in sigma (default: 1.0)
  --cutout_rsun CUTOUT_RSUN
                        Cutout radius for images (solar radii) (default: 10.0)
  --no_multiscale       Do not use multiscale CLEAN
  --no_solar_mask       Do not use solar disk mask for CLEANing
  --no_savemodel        Do no save model images
  --no_saveres          Do not save residual images
  --no_make_plots       Do not generate helioprojective plots

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   Fraction of available CPU to use (default: 0.8)
  --mem_frac MEM_FRAC   Fraction of available memory to use (default: 0.8)
  --jobid JOBID         Job ID for process tracking and logging (default: 0)

2. Perform primary beam correction of MWA primary beam, for a single image, use run-mwa-singlepbcor .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-singlepbcor [-h] [--MWA_PB_file MWA_PB_FILE]
                           [--sweetspot_file SWEETSPOT_FILE]
                           [--leakage_file LEAKAGE_FILE] [--iau_order]
                           [--gridpoint GRIDPOINT] [--restore]
                           [--pb_jones_file PB_JONES_FILE] [--save_pb]
                           [--interpolated] [--num_threads NUM_THREADS]
                           imagename metafits outfile

Correct images for MWA primary beam response

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  imagename             Name of the image file
  metafits              Name of the metafits file
  outfile               Output file name

###################
Advanced parameters
###################:
  --MWA_PB_file MWA_PB_FILE
                        MWA primary beam file
  --sweetspot_file SWEETSPOT_FILE
                        MWA primary beam sweetspot file path
  --leakage_file LEAKAGE_FILE
                        Leakage information file
  --iau_order           PB Jones in IAU order
  --gridpoint GRIDPOINT
                        MWA sweet spot pointing number
  --restore             Restore the primary beam correction
  --pb_jones_file PB_JONES_FILE
                        NumPy file of PB Jones matrices
  --save_pb             Save PB Jones matrices
  --interpolated        Use interpolated beam model

###################
Hardware resource management parameters
###################:
  --num_threads NUM_THREADS
                        Number of CPU threads to use

3. Perform primary beam corrections of MWA primary beam for all images in a directory, use run-mwa-pbcor .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-pbcor [-h] --metafits METAFITS [--workdir WORKDIR]
                     [--leakage_dir LEAKAGE_DIR] [--no_make_TB]
                     [--no_make_plots] [--restore] [--verbose] [--jobid JOBID]
                     [--cpu_frac CPU_FRAC] [--mem_frac MEM_FRAC]
                     imagedir

Correct all images for MWA full-pol averaged primary beam

options:
  -h, --help            show this help message and exit

###################
Essential parameters
###################:
  imagedir              Path to image directory
  --metafits METAFITS   Metafits file (default: None)
  --workdir WORKDIR     Path to work directory (default: )

###################
Advanced parameters
###################:
  --leakage_dir LEAKAGE_DIR
                        Leakage file directory (default: )
  --no_make_TB          Do not generate brightness temperature map
  --no_make_plots       Do not make png plots
  --restore             Restore primary beam correction
  --verbose             Verbose logs
  --jobid JOBID         Job ID for logging and PID tracking (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC   CPU usage fraction (default: 0.8)
  --mem_frac MEM_FRAC   Memory usage fraction (default: 0.8)

Ploting related CLI

1. To make diagnostic plots of measurement sets, use run-mwa-msplot .

Click here to see parameters

P-AIRCARS data directory and docker environment is not setup yet
usage: run-mwa-msplot [-h] [--verbose] [--jobid JOBID] [--cpu_frac CPU_FRAC]
                      [--mem_frac MEM_FRAC]
                      mslist workdir outdir

Make diagnostic plots of measurement sets

options:
  -h, --help           show this help message and exit

###################
Essential parameters
###################:
  mslist               Measurement set list (comma separated)
  workdir              Name of work directory
  outdir               Output directory

###################
Advanced parameters
###################:
  --verbose            Verbose logs
  --jobid JOBID        Job ID (default: 0)

###################
Hardware resource management parameters
###################:
  --cpu_frac CPU_FRAC  CPU fraction to use (default: 0.8)
  --mem_frac MEM_FRAC  Memory fraction to use (default: 0.8)